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1. Copy-number analysis from genome sequencing data of 11,754 rare-disease parent-child trios: A model for identifying autosomal recessive human gene knockouts including a novel gene for autosomal recessive retinopathy

Author

Eric Olinger, Ian J. Wilson, Sarah Orr, Miguel Barroso-Gil, Ruxandra Neatu, Denize Atan, John A. Sayer, John C. Ambrose, Prabhu Arumugam, Roel Bevers, Marta Bleda, Freya Boardman-Pretty, Christopher R. Boustred, Helen Brittain, Mark J. Caulfield, Georgia C. Chan, Greg Elgar, Tom Fowler, Adam Giess, Angela Hamblin, Shirley Henderson, Tim J.P. Hubbard, Rob Jackson, Louise J. Jones, Dalia Kasperaviciute, Melis Kayikci, Athanasios Kousathanas, Lea Lahnstein, Sarah E.A. Leigh, Ivonne U.S. Leong, Javier F. Lopez, Fiona Maleady-Crowe, Meriel McEntagart, Federico Minneci, Loukas Moutsianas, Michael Mueller, Nirupa Murugaesu, Anna C. Need, Peter O’Donovan, Chris A. Odhams, Christine Patch, Mariana Buongermino Pereira, Daniel Perez-Gil, John Pullinger, Tahrima Rahim, Augusto Rendon, Tim Rogers, Kevin Savage, Kushmita Sawant, Richard H. Scott, Afshan Siddiq, Alexander Sieghart, Samuel C. Smith, Alona Sosinsky, Alexander Stuckey, Mélanie Tanguy, Ana Lisa Taylor Tavares, Ellen R.A. Thomas, Simon R. Thompson, Arianna Tucci, Matthew J. Welland, Eleanor Williams, Katarzyna Witkowska, and Suzanne M. Wood

Subjects
CNV analysis, Genome sequencing, NPHP1, Retinopathy, SLC66A1, Genetics, QH426-470, Medicine
Abstract

Purpose: In parent-child trios with genome sequencing data, we investigated inherited biallelic deletions to identify known and novel genetic disorders. Methods: We developed a copy-number variations analysis pipeline based on autosomal genome sequencing read depth of Genomics England 100,000 Genomes Project data from 11,754 parent-child trios and additional 18,875 non-trios. A control cohort of 15,440 cancer patients provided independent deletion frequencies. Results: Autosomal recessive (AR) modeling detected 34 distinct rare deletions that were homozygous in the proband and heterozygous in both parents. These inherited biallelic deletions were only detected in 52 trios. These “knockout” regions included 37 genes, having among them 8 with an Online Mendelian Inheritance in Man AR annotation. Deletions of NPHP1, followed by OTOA, both within segmental duplications, were the only recurrent findings explaining phenotypes in a total of 10 and 3 patients, respectively. Recurrent heterozygous NPHP1 deletions were detected in 0.3%-0.5% of controls. We reviewed “knockout” patients for the remaining 29 genes without disease associations and identified SLC66A1 as a likely novel cause for AR rod-cone dystrophy in 4 families. Conclusion: A tailored copy-number variations analysis of genome sequencing trio data shows that biallelic inherited gene deletions are rare, with NPHP1 biallelic deletions causing nephronophthisis the leading finding. We propose SLC66A1 as a novel cause for AR retinopathy.

Published
2024
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2. Developing a National Newborn Genomes Program: An Approach Driven by Ethics, Engagement and Co-design

Author

Amanda Pichini, Arzoo Ahmed, Christine Patch, David Bick, Mathilde Leblond, Dalia Kasperaviciute, Dasha Deen, Simon Wilde, Sofia Garcia Noriega, Christella Matoko, Alice Tuff-Lacey, Chris Wigley, and Richard H. Scott

Subjects
newborn screening, whole genome sequencing, rare diseases, public health, ethics, public engagement, Genetics, QH426-470
Abstract

The transformative potential of whole genome sequencing (WGS) as a diagnostic tool in healthcare has been demonstrated by initiatives including the 100,000 Genomes Project and is now offered to certain patients in the National Health Service (NHS) in England. Building on these foundations, the utility of WGS in the newborn period can now be explored. Genomics England is working in partnership with NHS England and NHS Improvement and other healthcare, patient and public interest groups to design a research program embedded in the NHS to explore the potential challenges and implications of offering WGS in all newborns. The program will aim to: 1) evaluate the feasibility, utility and impact on the NHS of screening for childhood-onset rare actionable genetic conditions; 2) understand how, with consent, genomic and healthcare data could be used to enable research to develop new diagnostics and treatments; and 3) explore the implications of storing an individual’s genome for use over their lifetime. Recognizing the important practical, scientific and ethical questions that we must explore in dialogue with the public and experts, we are taking a collaborative, evidence-based and ethically deliberate approach to designing the program. An iterative co-design process including a nationwide public dialogue has identified emergent themes and ethical considerations which are the focus of the program’s design. These themes will be further developed through continued engagement with healthcare professionals, researchers, ethics experts, patient groups and the public, with an ongoing commitment to embedding ongoing ethics research and co-design into the delivery of the program.

Published
2022
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3. Newborn Screening by Genomic Sequencing: Opportunities and Challenges

Author

David Bick, Arzoo Ahmed, Dasha Deen, Alessandra Ferlini, Nicolas Garnier, Dalia Kasperaviciute, Mathilde Leblond, Amanda Pichini, Augusto Rendon, Aditi Satija, Alice Tuff-Lacey, and Richard H. Scott

Subjects
newborn, screening, genome, sequencing, Pediatrics, RJ1-570
Abstract

Newborn screening for treatable disorders is one of the great public health success stories of the twentieth century worldwide. This commentary examines the potential use of a new technology, next generation sequencing, in newborn screening through the lens of the Wilson and Jungner criteria. Each of the ten criteria are examined to show how they might be applied by programmes using genomic sequencing as a screening tool. While there are obvious advantages to a method that can examine all disease-causing genes in a single assay at an ever-diminishing cost, implementation of genomic sequencing at scale presents numerous challenges, some which are intrinsic to screening for rare disease and some specifically linked to genomics-led screening. In addition to questions specific to routine screening considerations, the ethical, communication, data management, legal, and social implications of genomic screening programmes require consideration.

Published
2022
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4. MECOM-associated syndrome: a heterogeneous inherited bone marrow failure syndrome with amegakaryocytic thrombocytopenia

Author

Manuela Germeshausen, Phil Ancliff, Jaime Estrada, Markus Metzler, Eva Ponstingl, Horst Rütschle, Dirk Schwabe, Richard H. Scott, Sule Unal, Angela Wawer, Bernward Zeller, and Matthias Ballmaier

Subjects
Specialties of internal medicine, RC581-951
Abstract

Abstract: Heterozygous mutations in MECOM (MDS1 and EVI1 complex locus) have been reported to be causative of a rare association of congenital amegakaryocytic thrombocytopenia and radioulnar synostosis. Here we report on 12 patients with congenital hypomegakaryocytic thrombocytopenia caused by MECOM mutations (including 10 novel mutations). The mutations affected different functional domains of the EVI1 protein. The spectrum of phenotypes was much broader than initially reported for the first 3 patients; we found familial as well as sporadic cases, and the clinical spectrum ranged from isolated radioulnar synostosis with no or mild hematological involvement to severe bone marrow failure without obvious skeletal abnormality. The clinical picture included radioulnar synostosis, bone marrow failure, clinodactyly, cardiac and renal malformations, B-cell deficiency, and presenile hearing loss. No single clinical manifestation was detected in all patients affected by MECOM mutations. Radioulnar synostosis and B-cell deficiency were observed only in patients with mutations affecting a short region in the C-terminal zinc finger domain of EVI1. We propose the term MECOM-associated syndrome for this heterogeneous hereditary disease and inclusion of MECOM sequencing in the diagnostic workup of congenital bone marrow failure.

Published
2018
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5. Late-Onset Autosomal Dominant Macular Degeneration Caused by Deletion of the CRX Gene

Author

Samar Yahya, Claire E.L. Smith, James A. Poulter, Martin McKibbin, Gavin Arno, Jamie Ellingford, Kati Kämpjärvi, Muhammad I. Khan, Frans P.M. Cremers, Alison J. Hardcastle, Bruce Castle, David H.W. Steel, Andrew R. Webster, Graeme C. Black, Mohammed E. El-Asrag, Manir Ali, Carmel Toomes, Chris F. Inglehearn, Stuart Ingram, Rachel Taylor, Forbes Manson, Panagiotis Sergouniotis, Nikolas Pontikos, Michael Cheetham, Alessia Fiorentino, Susan Downes, Jing Yu, Stephanie Halford, Suzanne Broadgate, Veronica van Heyningen, John C. Ambrose, Prabhu Arumugam, Roel Bevers, Marta Bleda, Freya Boardman-Pretty, Christopher R. Boustred, Helen Brittain, Mark J. Caulfield, Georgia C. Chan, Greg Elgar, Tom Fowler, Adam Giess, Angela Hamblin, Shirley Henderson, Tim J.P. Hubbard, Rob Jackson, Louise J. Jones, Dalia Kasperaviciute, Melis Kayikci, Athanasios Kousathanas, Lea Lahnstein, Sarah E.A. Leigh, Ivonne U.S. Leong, Javier F. Lopez, Fiona Maleady-Crowe, Meriel McEntagart, Federico Minneci, Loukas Moutsianas, Michael Mueller, Nirupa Murugaesu, Anna C. Need, Peter O’Donovan, Chris A. Odhams, Christine Patch, Mariana Buongermino Pereira, Daniel Perez-Gil, John Pullinger, Tahrima Rahim, Augusto Rendon, Tim Rogers, Kevin Savage, Kushmita Sawant, Richard H. Scott, Afshan Siddiq, Alexander Sieghart, Samuel C. Smith, Alona Sosinsky, Alexander Stuckey, Mélanie Tanguy, Ana Lisa Taylor Tavares, Ellen R.A. Thomas, Simon R. Thompson, Arianna Tucci, Matthew J. Welland, Eleanor Williams, Katarzyna Witkowska, and Suzanne M. Wood

Subjects
Ophthalmology, All institutes and research themes of the Radboud University Medical Center, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12]
Abstract

To characterize the phenotype observed in a case series with macular disease and determine the cause.Multicenter case series.Six families (7 patients) with sporadic or multiplex macular disease with onset at 20 to 78 years, and 1 patient with age-related macular degeneration.Patients underwent ophthalmic examination; exome, genome, or targeted sequencing; and/or polymerase chain reaction (PCR) amplification of the breakpoint, followed by cloning and Sanger sequencing or direct Sanger sequencing.Clinical phenotypes, genomic findings, and a hypothesis explaining the mechanism underlying disease in these patients.All 8 cases carried the same deletion encompassing the genes TPRX1, CRX, and SULT2A1, which was absent from 382 control individuals screened by breakpoint PCR and 13 096 Clinical Genetics patients with a range of other inherited conditions screened by array comparative genomic hybridization. Microsatellite genotypes showed that these 7 families are not closely related, but genotypes immediately adjacent to the deletion breakpoints suggest they may share a distant common ancestor.Previous studies had found that carriers for a single defective CRX allele that was predicted to produce no functional CRX protein had a normal ocular phenotype. Here, we show that CRX whole-gene deletion in fact does cause a dominant late-onset macular disease.

Published
2023
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6. The Human Phenotype Ontology in 2017.

Author

Sebastian Köhler 0001, Nicole A. Vasilevsky, Mark Engelstad, Erin Foster, Julie A. McMurry, Ségolène Aymé, Gareth Baynam, Susan M. Bello, Cornelius F. Boerkoel, Kym M. Boycott, Michael Brudno, Orion J. Buske, Patrick F. Chinnery, Valentina Cipriani, Laureen E. Connell, Hugh J. S. Dawkins, Laura E. DeMare, Andrew Devereau, Bert B. A. de Vries, Helen V. Firth, Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna Jähn, Roger James, Roland Krause, Stanley J. F. Laulederkind, Hanns Lochmüller, Gholson J. Lyon, Soichi Ogishima, Annie Olry, Willem H. Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H. Scott, Michael Segal 0002, Panagiotis I. Sergouniotis, Richard Sever, Cynthia L. Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W. M. Veltman, Tom Vulliamy, Jing Yu 0006, Julie von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O. B. Jacobsen, Tudor Groza, Damian Smedley, Christopher J. Mungall, Melissa A. Haendel, and Peter N. Robinson

Published
2017
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7. 100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care — Preliminary Report

Author

Gill Wilson, Anna de Burca, Marta Bleda, Lucy R. Wedderburn, Matthew Welland, Kathleen Stirrups, Valentina Cipriani, Kerrie Woods, Vijeya Ganesan, Susan Hill, Rosaline Quinlivan, Georgia Chan, Mehul T. Dattani, Robert McFarland, Graeme C.M. Black, Rutendo Mapeta, Augusto Rendon, Francesco Muntoni, James O.J. Davies, Mina Ryten, Rebecca E. Foulger, Arianna Tucci, Dina Halai, Tom Fowler, Noemi B.A. Roy, Sarah Leigh, Dragana Josifova, Philip Twiss, Ana L.T. Tavares, Zerin Hyder, Detlef Bockenhauer, Patrick Yu-Wai-Man, Lara Abulhoul, Nikolas Pontikos, Anthony T. Moore, Huw R. Morris, Patrick F. Chinnery, Nicholas W. Wood, Ellen A. Thomas, Shehla Mohammed, Sofia Douzgou, Tanya Lam, Kate Gibson, Robert Sarkany, Teofila Bueser, Wei Wei, Siddharth Banka, Alexander Broomfield, Hiva Fassihi, Nils Koelling, Carolyn Campbell, James Buchanan, Melita Irving, Sandrine Compeyrot-Lacassagne, Karola Rehmström, Austen Worth, Nikhil Thapar, Andrew R. Webster, Paul Brennan, Rita Horvath, Gavin Arno, Richard H Scott, Sam Malka, Andrew O.M. Wilkie, Sofie Ashford, Maria Bitner-Glindzicz, Jana Vandrovcova, William G. Newman, Caroline F. Wright, Andrew M. Schaefer, Roger F.L. James, Robert W. Taylor, Melanie Babcock, Arjune Sen, Emma Baple, Ellen M. McDonagh, Stephanie Grunewald, Loukas Moutsianas, Melissa A. Haendel, Olivera Spasic-Boskovic, Eleanor G. Seaby, Anna Need, Clarissa Pilkington, Sarah Wordsworth, Shamima Rahman, Christine Patch, Colin Wallis, Kristina Ibanez, Bishoy Habib, Eik Haraldsdottir, Huw B. Thomas, Razvan Sultana, Andrea H. Németh, Agata Wolejko, Claire Palles, Phil Beales, Adam C. Shaw, Letizia Vestito, Emily Li, Sarah Rose, Sarah Hunter, Angela Matchan, Genevieve Say, Dalia Kasperaviciute, Henry Houlden, Raymond T. O’Keefe, R. Andres Floto, Jill Clayton-Smith, John B. Taylor, Hywel J. Williams, Volker Straub, Val Davison, Helen Savage, John Chisholm, Eleanor Dewhurst, Charles Crichton, Andrea Haworth, Clare Turnbull, Carolyn Tregidgo, Carme Camps, Christopher Penkett, Emer O’Connor, Georgina Hall, Lyn S. Chitty, Sally Halsall, Andrew D. Mumford, Annette G. Wagner, Eleanor Williams, Mark Bale, Julius O. Jacobsen, Willem H. Ouwehand, Charu Deshpande, Gavin Burns, Smita Y. Patel, James Polke, Thiloka Ratnaike, Gavin Fuller, John Burn, Kenneth E. S. Poole, Emma Footitt, John R. Bradley, Suzanne Wood, Russell J. Grocock, Jenny C. Taylor, Louise Izatt, Kikkeri N. Naresh, Katherine R. Smith, Nigel Burrows, Katrina Newland, Peter N. Robinson, Sarju G. Mehta, Michael A. Simpson, Michael R. Barnes, Pilar Cacheiro, Olivia Niblock, Tracy Lester, Dimitris Polychronopoulos, Helen Brittain, John A. Sayer, Antonio Martin, Eshika Haque, Sean Humphray, Douglass M. Turnbull, Damian Smedley, Andrew Devereau, Stefan Gräf, Sian Ellard, Ivone U.S. Leong, Martin G. Reese, Matthias Wielscher, Louise C. Daugherty, Perry M. Elliott, F. Lucy Raymond, Cecilia Compton, David Bentley, Catherine Snow, James Welch, Frances Flinter, Dom McMullan, Mark J. Caulfield, Paul Aurora, Mark Gurnell, Mary Kasanicki, I. Karen Temple, Michel Michaelides, Deborah Ruddy, Leema Robert, Janice Yip, Grainne S. Gorman, Andrew C. Browning, Richard Quinton, Maureen Cleary, Jamie M. Ellingford, Angela Douglas, Christopher Boustred, and Investigators, The 100,000 Genomes Project Pilot

Subjects
Adult, Male, Proband, medicine.medical_specialty, Adolescent, Pilot Projects, Genomics, Polymerase Chain Reaction, Genome, State Medicine, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Health care, Human Phenotype Ontology, Humans, Medicine, Child, Exome sequencing, 030304 developmental biology, Family Characteristics, 0303 health sciences, Whole Genome Sequencing, Genome, Human, business.industry, Genetic Variation, Rare Diseases/diagnosis, General Medicine, Middle Aged, United Kingdom, 3. Good health, Child, Preschool, Family medicine, Medical genetics, Female, business, Bristol, 030217 neurology & neurosurgery, Rare disease
Abstract

BACKGROUND: The U.K. 100,000 Genomes Project is in the process of investigating the role of genome sequencing in patients with undiagnosed rare diseases after usual care and the alignment of this research with health care implementation in the U.K. National Health Service. Other parts of this project focus on patients with cancer and infection.METHODS: We conducted a pilot study involving 4660 participants from 2183 families, among whom 161 disorders covering a broad spectrum of rare diseases were present. We collected data on clinical features with the use of Human Phenotype Ontology terms, undertook genome sequencing, applied automated variant prioritization on the basis of applied virtual gene panels and phenotypes, and identified novel pathogenic variants through research analysis.RESULTS: Diagnostic yields varied among family structures and were highest in family trios (both parents and a proband) and families with larger pedigrees. Diagnostic yields were much higher for disorders likely to have a monogenic cause (35%) than for disorders likely to have a complex cause (11%). Diagnostic yields for intellectual disability, hearing disorders, and vision disorders ranged from 40 to 55%. We made genetic diagnoses in 25% of the probands. A total of 14% of the diagnoses were made by means of the combination of research and automated approaches, which was critical for cases in which we found etiologic noncoding, structural, and mitochondrial genome variants and coding variants poorly covered by exome sequencing. Cohortwide burden testing across 57,000 genomes enabled the discovery of three new disease genes and 19 new associations. Of the genetic diagnoses that we made, 25% had immediate ramifications for clinical decision making for the patients or their relatives.CONCLUSIONS: Our pilot study of genome sequencing in a national health care system showed an increase in diagnostic yield across a range of rare diseases. (Funded by the National Institute for Health Research and others.).

Published
2021
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8. Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution

Author

Elena Savva, Ivan Macciocca, Tiong Yang Tan, Victor S Lin, Ivone U.S. Leong, Mark J. Caulfield, Richard H. Scott, Ana Lisa Taylor Tavares, Crystle Lee, Kevin Savage, Kathryn N. North, Olivia Niblock, Christopher Boustred, Sarah Leigh, Arina Puzriakova, Ellen M. McDonagh, Alison Yeung, William Bellamy, Catherine E. Snow, Ellen R.A. Thomas, Antonio Rueda-Martin, Paul De Fazio, Bryony A. Thompson, Louise C. Daugherty, Helen K. Brittain, Eleanor Williams, Chirag Patel, Oliver Hofmann, Ain Roesley, Zornitza Stark, Jane Deller, Zandra C. Deans, Susan M. White, Rebecca E. Foulger, Lilian Downie, Sue Hill, Augusto Rendon, Sebastian Lunke, Meriel McEntagart, Oleg Gerasimenko, Lavinia Gordon, and Roman Valls

Subjects
Consensus, Computer science, Process (engineering), MEDLINE, Gene Expression, Harmonization, Terminology, Terminology as Topic, Gene panel, Genetics, Humans, Data Curation, Genetics (clinical), Australia, Genetic Diseases, Inborn, Molecular Sequence Annotation, Genomics, Resolution (logic), Mobile Applications, Data science, United Kingdom, Identification (information), Gene Ontology, Scale (social sciences), Perspective, Delivery of Health Care, Biomarkers
Abstract

Clinical validity assessments of gene-disease associations underpin analysis and reporting in diagnostic genomics, and yet wide variability exists in practice, particularly in use of these assessments for virtual gene panel design and maintenance. Harmonization efforts are hampered by the lack of agreed terminology, agreed gene curation standards, and platforms that can be used to identify and resolve discrepancies at scale. We undertook a systematic comparison of the content of 80 virtual gene panels used in two healthcare systems by multiple diagnostic providers in the United Kingdom and Australia. The process was enabled by a shared curation platform, PanelApp, and resulted in the identification and review of 2,144 discordant gene ratings, demonstrating the utility of sharing structured gene-disease validity assessments and collaborative discordance resolution in establishing national and international consensus.

Published
2021
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9. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

Author

Sebastian Köhler 0001, Sandra C. Doelken, Christopher J. Mungall, Sebastian Bauer 0002, Helen V. Firth, Isabelle Bailleul-Forestier, Graeme C. M. Black, Danielle L. Brown, Michael Brudno, Jennifer Campbell, David R. FitzPatrick, Janan T. Eppig, Andrew P. Jackson, Kathleen Freson, Marta Gîrdea, Ingo Helbig, Jane A. Hurst, Johanna Jähn, Laird G. Jackson, Anne M. Kelly, David H. Ledbetter, Sahar Mansour, Christa L. Martin, Celia Moss, Andrew D. Mumford, Willem H. Ouwehand, Soo-Mi Park, Erin Rooney Riggs, Richard H. Scott, Sanjay Sisodiya, Steven Van Vooren, Ronald J. Wapner, Andrew O. M. Wilkie, Caroline F. Wright, Anneke T. Vulto-van Silfhout, Nicole de Leeuw, Bert B. A. de Vries, Nicole L. Washington, Cynthia L. Smith, Monte Westerfield, Paul N. Schofield, Barbara J. Ruef, Georgios V. Gkoutos, Melissa A. Haendel, Damian Smedley, Suzanna E. Lewis, and Peter N. Robinson

Published
2014
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10. MED27, SLC6A7, and MPPE1 variants in a complex neurodevelopmental disorder with severe dystonia

Author

Kimberley M. Reid, Robert Spaull, Smrithi Salian, Katy Barwick, Esther Meyer, Juan Zhen, Hiromi Hirata, Diba Sheipouri, Hind Benkerroum, Kathleen M. Gorman, Apostolos Papandreou, Michael A. Simpson, Yoshinobu Hirano, Irene Farabella, Maya Topf, Detelina Grozeva, Keren Carss, Martin Smith, Hardev Pall, Peter Lunt, Susanna De Gressi, Erik‐Jan Kamsteeg, Tobias B. Haack, Lucinda Carr, Rita Guerreiro, Jose Bras, Eamonn R. Maher, Richard H. Scott, Robert J. Vandenberg, F. Lucy Raymond, Wui K. Chong, Sniya Sudhakar, Kshitij Mankad, Maarten E. Reith, Philippe M. Campeau, Robert J. Harvey, and Manju A. Kurian

Subjects
MPPE1, Movement Disorders, MED27, Proline, SLC6A7, Dystonia, Neurology, Dystonic Disorders, Neurodevelopmental Disorders, Animals, RNA, Neurology (clinical), Status dystonicus, Zebrafish
Abstract

BackgroundDespite advances in next generation sequencing technologies, the identification of variants of uncertain significance (VUS) can often hinder definitive diagnosis in patients with complex neurodevelopmental disorders.ObjectiveThe objective of this study was to identify and characterize the underlying cause of disease in a family with two children with severe developmental delay associated with generalized dystonia and episodic status dystonicus, chorea, epilepsy, and cataracts.MethodsCandidate genes identified by autozygosity mapping and whole-exome sequencing were characterized using cellular and vertebrate model systems.ResultsHomozygous variants were found in three candidate genes: MED27, SLC6A7, and MPPE1. Although the patients had features of MED27-related disorder, the SLC6A7 and MPPE1 variants were functionally investigated. SLC6A7 variant in vitro overexpression caused decreased proline transport as a result of reduced cell-surface expression, and zebrafish knockdown of slc6a7 exhibited developmental delay and fragile motor neuron morphology that could not be rescued by L-proline transporter–G396S RNA. Lastly, patient fibroblasts displayed reduced cell-surface expression of glycophosphatidylinositol-anchored proteins linked to MPPE1 dysfunction.ConclusionsWe report a family harboring a homozygous MED27 variant with additional loss-of-function SLC6A7 and MPPE1 gene variants, which potentially contribute to a blended phenotype caused by multilocus pathogenic variants. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society

Published
2022
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11. SOX11 variants cause a neurodevelopmental disorder with infrequent ocular malformations and hypogonadotropic hypogonadism and with distinct DNA methylation profile

Author

Reem Al-Jawahiri, Aidin Foroutan, Jennifer Kerkhof, Haley McConkey, Michael Levy, Sadegheh Haghshenas, Kathleen Rooney, Jasmin Turner, Debbie Shears, Muriel Holder, Henrietta Lefroy, Bruce Castle, Linda M. Reis, Elena V. Semina, Katherine Lachlan, Kate Chandler, Thomas Wright, Jill Clayton-Smith, Franziska Phan Hug, Nelly Pitteloud, Lucia Bartoloni, Sabine Hoffjan, Soo-Mi Park, Ajay Thankamony, Melissa Lees, Emma Wakeling, Swati Naik, Britta Hanker, Katta M. Girisha, Emanuele Agolini, Zampino Giuseppe, Ziegler Alban, Marine Tessarech, Boris Keren, Alexandra Afenjar, Christiane Zweier, Andre Reis, Thomas Smol, Yoshinori Tsurusaki, Okamoto Nobuhiko, Futoshi Sekiguchi, Naomi Tsuchida, Naomichi Matsumoto, Ikuyo Kou, Yoshiro Yonezawa, Shiro Ikegawa, Bert Callewaert, Megan Freeth, Lotte Kleinendorst, Alan Donaldson, Marielle Alders, Anne De Paepe, Bekim Sadikovic, Alisdair McNeill, Deborah Nickerson, Michael Bamshad, Suzanne Leal, John C. Ambrose, Prabhu Arumugam, Roel Bevers, Marta Bleda, Freya Boardman-Pretty, Christopher R. Boustred, Helen Brittain, Mark J. Caulfield, Georgia C. Chan, Greg Elgar, Tom Fowler, Adam Giess, Angela Hamblin, Shirley Henderson, Tim J.P. Hubbard, Rob Jackson, Louise J. Jones, Dalia Kasperaviciute, Melis Kayikci, Athanasios Kousathanas, Lea Lahnstein, Sarah E.A. Leigh, Ivonne U.S. Leong, Javier F. Lopez, null FionaMaleady-Crowe, Meriel McEntagart, Federico Minneci, Loukas Moutsianas, Michael Mueller, Nirupa Murugaesu, Anna C. Need, Peter O’Donovan, Chris A. Odhams, Christine Patch, Mariana Buongermino Pereira, Daniel Perez-Gil, John Pullinger, null TahrimaRahim, Augusto Rendon, null TimRogers, Kevin Savage, Kushmita Sawant, Richard H. Scott, Afshan Siddiq, Alexander Sieghart, Samuel C. Smith, Alona Sosinsky, Alexander Stuckey, Mélanie Tanguy, Ana Lisa Taylor Tavares, Ellen R.A. Thomas, Simon R. Thompson, Arianna Tucci, Matthew J. Welland, Eleanor Williams, Katarzyna Witkowska, Suzanne M. Wood, Human Genetics, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, ARD - Amsterdam Reproduction and Development, and ACS - Pulmonary hypertension & thrombosis

Subjects
EXPRESSION, MUTATIONS, FEATURES, Hypogonadism, disorder, DNA Methylation, Genome sequencing, Methylation, Article, SOXC Transcription Factors, Klinefelter Syndrome, Phenotype, Neurodevelopmental disorder, Neurodevelopmental Disorders, Exome Sequencing, SOX11, Medicine and Health Sciences, Neurodevelopmental, Humans, Exome, Genetics (clinical)
Abstract

Purpose: This study aimed to undertake a multidisciplinary characterization of the phenotype associated with SOX11 variants. Methods: Individuals with protein altering variants in SOX11 were identified through exome and genome sequencing and international data sharing. Deep clinical phenotyping was undertaken by referring clinicians. Blood DNA methylation was assessed using Infinium MethylationEPIC array. The expression pattern of SOX11 in developing human brain was defined using RNAscope. Results: We reported 38 new patients with SOX11 variants. Idiopathic hypogonadotropic hypogonadism was confirmed as a feature of SOX11 syndrome. A distinctive pattern of blood DNA methylation was identified in SOX11 syndrome, separating SOX11 syndrome from other BAFopathies. Conclusion: SOX11 syndrome is a distinct clinical entity with characteristic clinical features and episignature differentiating it from BAFopathies. (C) 2022 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics.

Published
2022

12. An online compendium of treatable genetic disorders

Author

Richard H Scott, David P. Bick, David Dimmock, Sarah L Bick, Tom Fowler, and Mark J. Caulfield

Subjects
0301 basic medicine, Computer science, Health Personnel, Inheritance Patterns, Disease, 030105 genetics & heredity, World Wide Web, 03 medical and health sciences, Rare Diseases, genetic diseases, Health care, Genetics, medicine, Humans, Genetics (clinical), Research Articles, Internet, Point (typography), treatment, business.industry, Mechanism (biology), Genetic disorder, mobile application, medicine.disease, Compendium, 030104 developmental biology, The Internet, business, Mobile device, Research Article
Abstract

More than 4,000 genes have been associated with recognizable Mendelian/monogenic diseases. When faced with a new diagnosis of a rare genetic disorder, health care providers increasingly turn to internet resources for information to understand the disease and direct care. Unfortunately, it can be challenging to find information concerning treatment for rare diseases as key details are scattered across a number of authoritative websites and numerous journal articles. The website and associated mobile device application described in this article begin to address this challenge by providing a convenient, readily available starting point to find treatment information. The site, Rx-genes.com (https://www.rx-genes.com/), is focused on those conditions where the treatment is directed against the mechanism of the disease and thereby alters the natural history of the disease. The website currently contains 633 disease entries that include references to disease information and treatment guidance, a brief summary of treatments, the inheritance pattern, a disease frequency (if known), nonmolecular confirmatory testing (if available), and a link to experimental treatments. Existing entries are continuously updated, and new entries are added as novel treatments appear in the literature.

Published
2020

13. KIF1A ‐related disorders in children: A wide spectrum of central and peripheral nervous system involvement

Author

Manju A. Kurian, Dora Steel, Francesco Muntoni, Sniya Sudhakar, Richard H Scott, Lucinda Carr, Kshitij Mankad, Alison Male, Tarishi Nemani, Marios Kaliakatsos, Athina Ververi, Spas Getov, Mary M. Reilly, Pinki Munot, and Catherine DeVile

Subjects
Adult, Male, Nervous system, Pediatrics, medicine.medical_specialty, Sensory axonal neuropathy, Kinesins, Primary Dysautonomias, Young Adult, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Atrophy, Central Nervous System Diseases, medicine, Humans, Spasticity, Child, Retrospective Studies, Dystonia, Spastic Paraplegia, Hereditary, business.industry, General Neuroscience, Infant, Peripheral Nervous System Diseases, Dysautonomia, medicine.disease, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Peripheral nervous system, Female, Neurology (clinical), medicine.symptom, business, 030217 neurology & neurosurgery
Abstract

KIF1A-related disorders (KRD) were first described in 2011 and the phenotypic spectrum has subsequently expanded to encompass a range of central and peripheral nervous system involvement. Here we present a case series demonstrating the range of clinical, neurophysiological, and radiological features which may occur in childhood-onset KRD. We report on all the children and young people seen at a single large tertiary centre. Data were collected through a retrospective case-notes review. Twelve individuals from 10 families were identified. Eight different mutations were present, including four novel mutations. Two patients displayed a very severe phenotype including congenital contractures, severe spasticity and/or dystonia, dysautonomia, severe sensorimotor polyneuropathy and optic atrophy, significant white matter changes on brain MRI, respiratory insufficiency, and complete lack of neurodevelopmental progress. The remaining 10 patients represented a spectrum of severity with common features including a movement disorder with spasticity and/or dystonia, subtle features of dysautonomia, sensory axonal neuropathy, varying degrees of optic atrophy and of learning and/or behavioural difficulties, and subtle or absent-but sometimes progressive-changes in white matter on MRI. Epilepsy was common among the more severely affected children. This case series demonstrates that KRD comprise a range of neurological disorders, with both the milder and the more severe forms combining central and peripheral (including autonomic) nervous system deficits.

Published
2020
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14. Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study

Author

Kristina Ibañez, James Polke, R Tanner Hagelstrom, Egor Dolzhenko, Dorota Pasko, Ellen Rachel Amy Thomas, Louise C Daugherty, Dalia Kasperaviciute, Katherine R Smith, Zandra C Deans, Sue Hill, Tom Fowler, Richard H Scott, John Hardy, Patrick F Chinnery, Henry Houlden, Augusto Rendon, Mark J Caulfield, Michael A Eberle, Ryan J Taft, Arianna Tucci, Ellen M McDonagh, Antonio Rueda, Dimitris Polychronopoulos, Georgia Chan, Heather Angus-Leppan, Kailash P Bhatia, James E Davison, Richard Festenstein, Pietro Fratta, Paola Giunti, Robin Howard, Laxmi Venkata, Matilde Laurá, Meriel McEntagart, Lara Menzies, Huw Morris, Mary M Reilly, Robert Robinson, Elisabeth Rosser, Francesca Faravelli, Anette Schrag, Jonathan M Schott, Thomas T Warner, Nicholas W Wood, David Bourn, Kelly Eggleton, Robyn Labrum, Philip Twiss, Stephen Abbs, Liana Santos, Ghareesa Almheiri, Isabella Sheikh, Jana Vandrovcova, Christine Patch, Ana Lisa Taylor Tavares, Zerin Hyder, Anna Need, Helen Brittain, Emma Baple, Loukas Moutsianas, Viraj Deshpande, Denise L Perry, Subramanian S. Ajay, Aditi Chawla, Vani Rajan, Kathryn Oprych, Angela Douglas, Gill Wilson, Sian Ellard, I Karen Temple, Andrew Mumford, Dom McMullan, Kikkeri Naresh, Frances A Flinter, Jenny C Taylor, Lynn Greenhalgh, William Newman, Paul Brennan, John A Sayer, F Lucy Raymond, Lyn S Chitty, John C. Ambrose, Prabhu Arumugam, Marta Bleda, Freya Boardman-Pretty, Jeanne M. Boissiere, Christopher R. Boustred, Clare E.H. Craig, Anna de Burca, Andrew Devereau, Greg Elgar, Rebecca E. Foulger, Pedro Furió-Tarí, Joanne Hackett, Dina Halai, Angela Hamblin, Shirley Henderson, James Holman, Tim J.P. Hubbard, Rob Jackson, Louise J. Jones, Melis Kayikci, Lea Lahnstein, Kay Lawson, Sarah E.A. Leigh, Ivonne U.S. Leong, Javier F. Lopez, Fiona Maleady-Crowe, Joanne Mason, Michael Mueller, Nirupa Murugaesu, Chris A. Odhams, Daniel Perez-Gil, John Pullinger, Tahrima Rahim, Pablo Riesgo-Ferreiro, Tim Rogers, Mina Ryten, Kevin Savage, Kushmita Sawant, Afshan Siddiq, Alexander Sieghart, Damian Smedley, Alona Sosinsky, William Spooner, Helen E. Stevens, Alexander Stuckey, Razvan Sultana, Simon R. Thompson, Carolyn Tregidgo, Emma Walsh, Sarah A. Watters, Matthew J. Welland, Eleanor Williams, Katarzyna Witkowska, Suzanne M. Wood, and Magdalena Zarowiecki

Subjects
Fragile X Mental Retardation Protein, DNA Repeat Expansion, Whole Genome Sequencing, Whole Genome Sequencing/methods, Humans, Neurology (clinical), Prospective Studies, Child, Fragile X Mental Retardation Protein/genetics, State Medicine, United Kingdom, Retrospective Studies
Abstract

BACKGROUND: Repeat expansion disorders affect about 1 in 3000 individuals and are clinically heterogeneous diseases caused by expansions of short tandem DNA repeats. Genetic testing is often locus-specific, resulting in underdiagnosis of people who have atypical clinical presentations, especially in paediatric patients without a previous positive family history. Whole genome sequencing is increasingly used as a first-line test for other rare genetic disorders, and we aimed to assess its performance in the diagnosis of patients with neurological repeat expansion disorders.METHODS: We retrospectively assessed the diagnostic accuracy of whole genome sequencing to detect the most common repeat expansion loci associated with neurological outcomes (AR, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, C9orf72, CACNA1A, DMPK, FMR1, FXN, HTT, and TBP) using samples obtained within the National Health Service in England from patients who were suspected of having neurological disorders; previous PCR test results were used as the reference standard. The clinical accuracy of whole genome sequencing to detect repeat expansions was prospectively examined in previously genetically tested and undiagnosed patients recruited in 2013-17 to the 100 000 Genomes Project in the UK, who were suspected of having a genetic neurological disorder (familial or early-onset forms of ataxia, neuropathy, spastic paraplegia, dementia, motor neuron disease, parkinsonian movement disorders, intellectual disability, or neuromuscular disorders). If a repeat expansion call was made using whole genome sequencing, PCR was used to confirm the result.FINDINGS: The diagnostic accuracy of whole genome sequencing to detect repeat expansions was evaluated against 793 PCR tests previously performed within the NHS from 404 patients. Whole genome sequencing correctly classified 215 of 221 expanded alleles and 1316 of 1321 non-expanded alleles, showing 97·3% sensitivity (95% CI 94·2-99·0) and 99·6% specificity (99·1-99·9) across the 13 disease-associated loci when compared with PCR test results. In samples from 11 631 patients in the 100 000 Genomes Project, whole genome sequencing identified 81 repeat expansions, which were also tested by PCR: 68 were confirmed as repeat expansions in the full pathogenic range, 11 were non-pathogenic intermediate expansions or premutations, and two were non-expanded repeats (16% false discovery rate).INTERPRETATION: In our study, whole genome sequencing for the detection of repeat expansions showed high sensitivity and specificity, and it led to identification of neurological repeat expansion disorders in previously undiagnosed patients. These findings support implementation of whole genome sequencing in clinical laboratories for diagnosis of patients who have a neurological presentation consistent with a repeat expansion disorder.FUNDING: Medical Research Council, Department of Health and Social Care, National Health Service England, National Institute for Health Research, and Illumina.

Published
2022
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15. Clinical and Functional Characterization of the Recurrent TUBA1A p.(Arg2His) Mutation

Author

Jennifer F. Gardner, Thomas D. Cushion, Georgios Niotakis, Heather E. Olson, P. Ellen Grant, Richard H. Scott, Neil Stoodley, Julie S. Cohen, Sakkubai Naidu, Tania Attie-Bitach, Maryse Bonnières, Lucile Boutaud, Férechté Encha-Razavi, Sheila M. Palmer-Smith, Hood Mugalaasi, Jonathan G. L. Mullins, Daniela T. Pilz, and Andrew E. Fry

Subjects
TUBA1A, tubulin, p.(Arg2His), R2H, tubulinopathy, polymicrogyria, cerebellar hypoplasia, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract

The TUBA1A gene encodes tubulin alpha-1A, a protein that is highly expressed in the fetal brain. Alpha- and beta-tubulin subunits form dimers, which then co-assemble into microtubule polymers: dynamic, scaffold-like structures that perform key functions during neurogenesis, neuronal migration, and cortical organisation. Mutations in TUBA1A have been reported to cause a range of brain malformations. We describe four unrelated patients with the same de novo missense mutation in TUBA1A, c.5G>A, p.(Arg2His), as found by next generation sequencing. Detailed comparison revealed similar brain phenotypes with mild variability. Shared features included developmental delay, microcephaly, hypoplasia of the cerebellar vermis, dysplasia or thinning of the corpus callosum, small pons, and dysmorphic basal ganglia. Two of the patients had bilateral perisylvian polymicrogyria. We examined the effects of the p.(Arg2His) mutation by computer-based protein structure modelling and heterologous expression in HEK-293 cells. The results suggest the mutation subtly impairs microtubule function, potentially by affecting inter-dimer interaction. Based on its sequence context, c.5G>A is likely to be a common recurrent mutation. We propose that the subtle functional effects of p.(Arg2His) may allow for other factors (such as genetic background or environmental conditions) to influence phenotypic outcome, thus explaining the mild variability in clinical manifestations.

Published
2018
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16. Author response for 'Biallelic TMEM260 variants cause Truncus Arteriosus, with or without renal defects'

Author

null Alistair T. Pagnamenta, null Adam Jackson, null Rahat Perveen, null Glenda Beaman, null Gemma Petts, null Asheeta Gupta, null Zerin Hyder, null Brian Hon‐Yin Chung, null Anita Sik‐Yau Kan, null Ka Wang Cheung, null Wilhelmina S. Kerstjens‐Frederikse, null Kristin M. Abbott, null John C. Ambrose, null Prabhu Arumugam, null Roel Bevers, null Marta Bleda, null Freya Boardman‐Pretty, null Christopher R. Boustred, null Helen Brittain, null Mark J. Caulfield, null Georgia C. Chan, null Greg Elgar, null Tom Fowler, null Adam Giess, null Angela Hamblin, null Shirley Henderson, null Tim J. P. Hubbard, null Rob Jackson, null Louise J. Jones, null Dalia Kasperaviciute, null Melis Kayikci, null Athanasios Kousathanas, null Lea Lahnstein, null Sarah E. A. Leigh, null Ivonne U. S. Leong, null Javier F. Lopez, null Fiona Maleady‐Crowe, null Meriel McEntagart, null Federico Minneci, null Loukas Moutsianas, null Michael Mueller, null Nirupa Murugaesu, null Anna C. Need, null Peter O′Donovan, null Chris A. Odhams, null Christine Patch, null Mariana Buongermino Pereira, null Daniel Perez‐Gil, null John Pullinger, null Tahrima Rahim, null Augusto Rendon, null Tim Rogers, null Kevin Savage, null Kushmita Sawant, null Richard H. Scott, null Afshan Siddiq, null Alexander Sieghart, null Samuel C. Smith, null Alona Sosinsky, null Alexander Stuckey, null Mélanie Tanguy, null Ana Lisa Taylor Tavares, null Ellen R. A. Thomas, null Simon R. Thompson, null Arianna Tucci, null Matthew J. Welland, null Eleanor Williams, null Katarzyna Witkowska, null Suzanne M. Wood, null Orly Elpeleg, null Jenny C. Taylor, null Siddharth Banka, null Asaf Ta‐Shma, and null Genomics England Research Consortium

Subjects
medicine.medical_specialty, business.industry, Internal medicine, Cardiology, medicine, business, Truncus arteriosus
Published
2021
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17. Whole genome sequencing identifies multiple loci for critical illness caused by COVID-19

Author

Clark D Russell, Erola Pairo-Castineira, Malcolm G Semple, James F. Wilson, Jian Yang, andMe Investigators, Seán Keating, Yang Wu, Tala Zainy, Greg Elgar, Angie Fawkes, Lucija Klaric, Julian C. Knight, Paul Elliott, Richard H Scott, Charlotte Summers, David M. Maslove, Daniel F. McAuley, Marie Zechner, Sally Donovan, J Kenneth Baillie, Athanasios Kousathanas, Daniel Rhodes, Nicholas J. Parkinson, Veronique Vitart, Susan P. Walker, Peter Horby, Fiona Griffiths, Bo Wang, Peter J. M. Openshaw, Linda Todd, Andy Law, Sara Clohisey, Tom Fowler, Augusto Rendon, Alex Stuckey, Christopher A Odhams, Andrew D. Bretherick, Hugh Montgomery, Katherine S. Elliott, Shahla Salehi, Jonathan E Millar, Loukas Moutsianas, Charles J. Hinds, Kathy Rowan, Mark J. Caulfield, Fiona Maleady-Crowe, Timothy S. Walsh, Prabhu Arumugam, Georgia Chan, Lee Murphy, Afshan Siddiq, GenoMICC Investigators, Tomas Malinauskas, Konrad Rawlik, Kirstie Morrice, Chris P. Ponting, Alistair Nichol, Wilna Oosthuyzen, Manu Shankar-Hari, and Peter Goddard

Subjects
Whole genome sequencing, Genetics, education.field_of_study, Immune system, Antigen, Genetic variation, Population, Disease, Biology, Lung injury, education, Gene
Abstract

Critical illness in COVID-19 is caused by inflammatory lung injury, mediated by the host immune system. We and others have shown that host genetic variation influences the development of illness requiring critical care1or hospitalisation2;3;4following SARS-Co-V2 infection. The GenOMICC (Genetics of Mortality in Critical Care) study recruits critically-ill cases and compares their genomes with population controls in order to find underlying disease mechanisms.Here, we use whole genome sequencing and statistical fine mapping in 7,491 critically-ill cases compared with 48,400 population controls to discover and replicate 22 independent variants that significantly predispose to life-threatening COVID-19. We identify 15 new independent associations with critical COVID-19, including variants within genes involved in interferon signalling (IL10RB, PLSCR1), leucocyte differentiation (BCL11A), and blood type antigen secretor status (FUT2). Using transcriptome-wide association and colocalisation to infer the effect of gene expression on disease severity, we find evidence implicating expression of multiple genes, including reduced expression of a membrane flippase (ATP11A), and increased mucin expression (MUC1), in critical disease.We show that comparison between critically-ill cases and population controls is highly efficient for genetic association analysis and enables detection of therapeutically-relevant mechanisms of disease. Therapeutic predictions arising from these findings require testing in clinical trials.

Published
2021
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18. Phenotypic expansion ofPOGZ‐related intellectual disability syndrome (White‐Sutton syndrome)

Author

V. Reid Sutton, Katelyn Payne, Emily Chen, Xiaofei Song, Annick Raas-Rothschild, Elizabeth Mizerik, Shannon Holtrop, Margarita Nieto Moreno, Chester W. Brown, Nurit Assia Batzir, James R. Lupski, Richard H Scott, Jennifer E. Posey, Hilary J. Vernon, Neda Zadeh, Zeynep Coban Akdemir, and Jill A. Rosenfeld

Subjects
Adult, Male, Heterozygote, Microcephaly, Pediatrics, medicine.medical_specialty, Adolescent, Hearing loss, Population, Transposases, Article, Young Adult, Intellectual Disability, Exome Sequencing, Intellectual disability, Genetics, medicine, Humans, Exome, Language Development Disorders, Autistic Disorder, Child, education, Genetics (clinical), Exome sequencing, education.field_of_study, business.industry, Infant, Middle Aged, medicine.disease, Obstructive sleep apnea, Phenotype, Child, Preschool, Mutation, Speech delay, Autism, Female, medicine.symptom, business
Abstract

White-Sutton syndrome (WHSUS) is a recently-identified genetic disorder resulting from de novo heterozygous pathogenic variants in POGZ. Thus far, over 50 individuals have been reported worldwide, however phenotypic characterization and data regarding the natural history are still incomplete. Here we report the clinical features of 22 individuals with 21 unique loss of function POGZ variants. We observed a broad spectrum of intellectual disability and/or developmental delay with or without autism, and speech delay in all individuals. Other common problems included ocular abnormalities, hearing loss and gait abnormalities. A validated sleep disordered breathing questionnaire identified symptoms of obstructive sleep apnea in 4/12 (33%) individuals. A higher-than-expected proportion of cases also had gastrointestinal phenotypes, both functional and anatomical, as well as genitourinary anomalies. In line with previous publications, we observed an increased body mass index (BMI) z-score compared to the general population (mean 0.59, median 0.9; p 0.0253). Common facial features included microcephaly, broad forehead, midface hypoplasia, triangular mouth, broad nasal root and flat nasal bridge. Analysis of the Baylor Genetics clinical laboratory database revealed that POGZ variants were implicated in approximately 0.14% of cases who underwent clinical exome sequencing for neurological indications with or without involvement of other body systems. This study describes a greater allelic series and expands the phenotypic spectrum of this new syndromic form of intellectual disability and autism.

Published
2019
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19. PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels

Author

Arianna Tucci, Mark J. Caulfield, Eik Haraldsdottir, Damian Smedley, Kristina Ibáñez, Sarah Leigh, Olivia Niblock, Antonio Rueda Martin, Ivone U. S. Leong, Anna de Burca, Eleanor Williams, Rebecca E. Foulger, Richard H Scott, Ellen M. McDonagh, Emma L. Baple, Louise C. Daugherty, Katherine R. Smith, Ellen Thomas, D. Kasperaviciute, Augusto Rendon, Oleg Gerasimenko, and Helen Brittain

Subjects
Crowdsource, Knowledge base, business.industry, Gene panel, Genetics, MEDLINE, Causation, Biology, business, Crowdsourcing, Data science
Abstract

A fundamental problem in rare-disease diagnostics is the lack of consensus as to which genes have sufficient evidence to attribute causation. To address this issue, we have created PanelApp ( https://panelapp.genomicsengland.co.uk ), a publicly available knowledge base of curated virtual gene panels.

Published
2019
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20. Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data

Author

Stuart Aitken, Helen V. Firth, Jeremy McRae, Mihail Halachev, Usha Kini, Michael J. Parker, Melissa M. Lees, Katherine Lachlan, Ajoy Sarkar, Shelagh Joss, Miranda Splitt, Shane McKee, Andrea H. Németh, Richard H. Scott, Caroline F. Wright, Joseph A. Marsh, Matthew E. Hurles, David R. FitzPatrick, T.W. Fitzgerald, S.S. Gerety, W.D. Jones, M. van Kogelenberg, D.A. King, J. McRae, K.I. Morley, V. Parthiban, S. Al-Turki, K. Ambridge, D.M. Barrett, T. Bayzetinova, S. Clayton, E.L. Coomber, S. Gribble, P. Jones, N. Krishnappa, L.E. Mason, A. Middleton, R. Miller, E. Prigmore, D. Rajan, A. Sifrim, A.R. Tivey, M. Ahmed, N. Akawi, R. Andrews, U. Anjum, H. Archer, R. Armstrong, M. Balasubramanian, R. Banerjee, D. Barelle, P. Batstone, D. Baty, C. Bennett, J. Berg, B. Bernhard, A.P. Bevan, E. Blair, M. Blyth, D. Bohanna, L. Bourdon, D. Bourn, A. Brady, E. Bragin, C. Brewer, L. Brueton, K. Brunstrom, S.J. Bumpstead, D.J. Bunyan, J. Burn, J. Burton, N. Canham, B. Castle, K. Chandler, S. Clasper, J. Clayton-Smith, T. Cole, A. Collins, M.N. Collinson, F. Connell, N. Cooper, H. Cox, L. Cresswell, G. Cross, Y. Crow, P.M. D’Alessandro, T. Dabir, R. Davidson, S. Davies, J. Dean, C. Deshpande, G. Devlin, A. Dixit, A. Dominiczak, C. Donnelly, D. Donnelly, A. Douglas, A. Duncan, J. Eason, S. Edkins, S. Ellard, P. Ellis, F. Elmslie, K. Evans, S. Everest, T. Fendick, R. Fisher, F. Flinter, N. Foulds, A. Fryer, B. Fu, C. Gardiner, L. Gaunt, N. Ghali, R. Gibbons, S.L. Gomes Pereira, J. Goodship, D. Goudie, E. Gray, P. Greene, L. Greenhalgh, L. Harrison, R. Hawkins, S. Hellens, A. Henderson, E. Hobson, S. Holden, S. Holder, G. Hollingsworth, T. Homfray, M. Humphreys, J. Hurst, S. Ingram, M. Irving, J. Jarvis, L. Jenkins, D. Johnson, D. Jones, E. Jones, D. Josifova, S. Joss, B. Kaemba, S. Kazembe, B. Kerr, U. Kini, E. Kinning, G. Kirby, C. Kirk, E. Kivuva, A. Kraus, D. Kumar, K. Lachlan, W. Lam, A. Lampe, C. Langman, M. Lees, D. Lim, G. Lowther, S.A. Lynch, A. Magee, E. Maher, S. Mansour, K. Marks, K. Martin, U. Maye, E. McCann, V. McConnell, M. McEntagart, R. McGowan, K. McKay, S. McKee, D.J. McMullan, S. McNerlan, S. Mehta, K. Metcalfe, E. Miles, S. Mohammed, T. Montgomery, D. Moore, S. Morgan, A. Morris, J. Morton, H. Mugalaasi, V. Murday, L. Nevitt, R. Newbury-Ecob, A. Norman, R. O’Shea, C. Ogilvie, S. Park, M.J. Parker, C. Patel, J. Paterson, S. Payne, J. Phipps, D.T. Pilz, D. Porteous, N. Pratt, K. Prescott, S. Price, A. Pridham, A. Proctor, H. Purnell, N. Ragge, J. Rankin, L. Raymond, D. Rice, L. Robert, E. Roberts, G. Roberts, J. Roberts, P. Roberts, A. Ross, E. Rosser, A. Saggar, S. Samant, R. Sandford, A. Sarkar, S. Schweiger, C. Scott, R. Scott, A. Selby, A. Seller, C. Sequeira, N. Shannon, S. Sharif, C. Shaw-Smith, E. Shearing, D. Shears, I. Simonic, D. Simpkin, R. Singzon, Z. Skitt, A. Smith, B. Smith, K. Smith, S. Smithson, L. Sneddon, M. Splitt, M. Squires, F. Stewart, H. Stewart, M. Suri, V. Sutton, G.J. Swaminathan, E. Sweeney, K. Tatton-Brown, C. Taylor, R. Taylor, M. Tein, I.K. Temple, J. Thomson, J. Tolmie, A. Torokwa, B. Treacy, C. Turner, P. Turnpenny, C. Tysoe, A. Vandersteen, P. Vasudevan, J. Vogt, E. Wakeling, D. Walker, J. Waters, A. Weber, D. Wellesley, M. Whiteford, S. Widaa, S. Wilcox, D. Williams, N. Williams, G. Woods, C. Wragg, M. Wright, F. Yang, M. Yau, N.P. Carter, M. Parker, H.V. Firth, D.R. FitzPatrick, C.F. Wright, J.C. Barrett, and M.E. Hurles

Subjects
Male, 0301 basic medicine, Proband, Nonsynonymous substitution, Heterozygote, phenotype, Developmental Disabilities, genotype, Dwarfism, Biology, Article, naive Bayes, 03 medical and health sciences, 0302 clinical medicine, Gene Frequency, Similarity (network science), developmental disease, Exome Sequencing, Genotype, Genetics, medicine, Humans, tSNE, Exome, Genetic Predisposition to Disease, Child, Gene, Allele frequency, Genetics (clinical), Spectrin, Bayes Theorem, medicine.disease, Repressor Proteins, Developmental disorder, 030104 developmental biology, Mutation, Mutation (genetic algorithm), Female, 030217 neurology & neurosurgery
Abstract

Trio-based whole-exome sequence (WES) data have established confident genetic diagnoses in ∼40% of previously undiagnosed individuals recruited to the Deciphering Developmental Disorders (DDD) study. Here we aim to use the breadth of phenotypic information recorded in DDD to augment diagnosis and disease variant discovery in probands. Median Euclidean distances (mEuD) were employed as a simple measure of similarity of quantitative phenotypic data within sets of ≥10 individuals with plausibly causative de novo mutations (DNM) in 28 different developmental disorder genes. 13/28 (46.4%) showed significant similarity for growth or developmental milestone metrics, 10/28 (35.7%) showed similarity in HPO term usage, and 12/28 (43%) showed no phenotypic similarity. Pairwise comparisons of individuals with high-impact inherited variants to the 32 individuals with causative DNM in ANKRD11 using only growth z-scores highlighted 5 likely causative inherited variants and two unrecognized DNM resulting in an 18% diagnostic uplift for this gene. Using an independent approach, naive Bayes classification of growth and developmental data produced reasonably discriminative models for the 24 DNM genes with sufficiently complete data. An unsupervised naive Bayes classification of 6,993 probands with WES data and sufficient phenotypic information defined 23 in silico syndromes (ISSs) and was used to test a “phenotype first” approach to the discovery of causative genotypes using WES variants strictly filtered on allele frequency, mutation consequence, and evidence of constraint in humans. This highlighted heterozygous de novo nonsynonymous variants in SPTBN2 as causative in three DDD probands.

Published
2019
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21. Evaluating the performance of a clinical genome sequencing program for diagnosis of rare genetic disease, seen through the lens of craniosynostosis

Author

Zerin Hyder, Eduardo Calpena, Yang Pei, Rebecca S. Tooze, Helen Brittain, Stephen R.F. Twigg, Deirdre Cilliers, Jenny E.V. Morton, Emma McCann, Astrid Weber, Louise C. Wilson, Andrew G.L. Douglas, Ruth McGowan, Anna Need, Andrew Bond, Ana Lisa Taylor Tavares, Ellen R.A. Thomas, John C. Ambrose, Prabhu Arumugam, Roel Bevers, Marta Bleda, Christopher R. Boustred, Georgia C. Chan, Greg Elgar, Tom Fowler, Adam Giess, Angela Hamblin, Shirley Henderson, Tim J.P. Hubbard, Rob Jackson, Louise J. Jones, Dalia Kasperaviciute, Melis Kayikci, Athanasios Kousathanas, Lea Lahnstein, Sarah E.A. Leigh, Ivonne U.S. Leong, Javier F. Lopez, Fiona Maleady-Crowe, Meriel McEntagart, Federico Minneci, Loukas Moutsianas, Michael Mueller, Nirupa Murugaesu, Peter O’Donovan, Chris A. Odhams, Christine Patch, Mariana Buongermino Pereira, Daniel Perez-Gil, John Pullinger, Tahrima Rahim, Augusto Rendon, Tim Rogers, Kevin Savage, Kushmita Sawant, Afshan Siddiq, Alexander Sieghart, Samuel C. Smith, Alona Sosinsky, Alexander Stuckey, Mélanie Tanguy, Simon R. Thompson, Arianna Tucci, Matthew J. Welland, Eleanor Williams, Katarzyna Witkowska, Suzanne M. Wood, Susan L. Hill, Zandra C. Deans, Freya Boardman-Pretty, Mark Caulfield, Richard H. Scott, and Andrew O.M. Wilkie

Subjects
Proband, medicine.diagnostic_test, Base Sequence, business.industry, Chromosome Mapping, Genomics, Disease, Bioinformatics, medicine.disease, Genome, DNA sequencing, Article, Craniosynostosis, Craniosynostoses, Rare Diseases, medicine, Humans, Genetic Testing, Medical diagnosis, business, Genetics (clinical), Genetic testing
Abstract

PurposeGenome sequencing (GS) for diagnosis of rare genetic disease is being introduced into the clinic, but the complexity of the data poses challenges for developing pipelines with high diagnostic sensitivity. We evaluated the performance of the Genomics England 100,000 Genomes Project (100kGP) panel-based pipelines, using craniosynostosis as a test disease.MethodsGS data from 114 probands with craniosynostosis and their relatives (314 samples), negative on routine genetic testing, were scrutinized by a specialized research team, and diagnoses compared with those made by 100kGP.ResultsSixteen likely pathogenic/pathogenic variants were identified by 100kGP. Eighteen additional likely pathogenic/pathogenic variants were identified by the research team, indicating that for craniosynostosis, 100kGP panels had a diagnostic sensitivity of only 47%. Measures that could have augmented diagnoses were improved calling of existing panel genes (+18% sensitivity), review of updated panels (+12%), comprehensive analysis of de novo small variants (+29%), and copy-number/structural variants (+9%). Recent NHS England recommendations that partially incorporate these measures should achieve 85% overall sensitivity (+38%).ConclusionGS identified likely pathogenic/pathogenic variants in 29.8% of previously undiagnosed patients with craniosynostosis. This demonstrates the value of research analysis and the importance of continually improving algorithms to maximize the potential of clinical GS.

Published
2021
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22. Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals

Author

Martin I. Jones, Joseph D. Szustakowski, Giorgio Sirugo, Lukas Habegger, Adam J. Mansfield, Will Salerno, Joshua D. Backman, Athanasios Kousathanas, David J. Carey, Yi-Pin Lai, James F. Wilson, Alison M. Meynert, Anne E. Justice, Alexander H. Li, Jack A. Kosmicki, Anthony Marcketta, Sándor Szalma, Shane McCarthy, A. R. Shuldiner, A. Baras, Daniel J. Rader, Michael N. Cantor, Ashish Yadav, Manuel A. R. Ferreira, F. S. P. Kury, Konrad Rawlik, Loukas Moutsianas, Gonçalo R. Abecasis, Susan P. Walker, Xing Chen, Albert Tenesa, Paul Nioi, Adam E. Locke, Guillaume Butler-Laporte, E. N. Smith, Richard H Scott, Gundula Povysil, Joseph B. Leader, Lauren Gurski, Dorota Pasko, Marylyn D. Ritchie, A. Cordova-Palomera, Kyoko Watanabe, Colm O'Dushlaine, A. O'Neill, Tomoko Nakanishi, Erola Pairo-Castineira, Xiuwen Zheng, Emily Wong, Jeffrey G. Reid, Slavé Petrovski, Julie E. Horowitz, Anurag Verma, Justin W. Davis, Dylan Sun, Sahar Esmaeeli, Heiko Runz, Quanli Wang, John D. Overton, Shareef Khalid, Tooraj Mirshahi, Evan Maxwell, Mark J. Caulfield, Mark Lathrop, Olympe Chazara, Deepika Sharma, David Goldstein, Jonathan Marchini, Xiaodong Bai, Suganthi Balasubramanian, Krzysztof Kiryluk, Nilanjana Banerjee, Rouel Lanche, J. B. Richards, Hyun Min Kang, J. K. Baillie, Yunfeng Huang, Sean O'Keeffe, Erika Kvikstad, Margaret M. Parker, and Joelle Mbatchou

Subjects
Male, 0301 basic medicine, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Biology, 03 medical and health sciences, Current sample, 0302 clinical medicine, Data sequences, Report, Exome Sequencing, Genetics, Humans, Exome, Genetic Predisposition to Disease, 030212 general & internal medicine, Gene, Genetics (clinical), SARS-CoV-2, COVID-19, Prognosis, Hospitalization, 030104 developmental biology, Sample Size, Multiple comparisons problem, Susceptibility locus, Female, Interferons
Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a respiratory illness that can result in hospitalization or death. We used exome sequence data to investigate associations between rare genetic variants and seven COVID-19 outcomes in 586,157 individuals, including 20,952 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome wide or when specifically focusing on (1) 13 interferon pathway genes in which rare deleterious variants have been reported in individuals with severe COVID-19, (2) 281 genes located in susceptibility loci identified by the COVID-19 Host Genetics Initiative, or (3) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, and results are publicly available through the Regeneron Genetics Center COVID-19 Results Browser.

Published
2021
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23. Diagnosing Mitochondrial Disorders Remains Challenging in the Omics Era

Author

Cathy E. Woodward, Thomas S. Jacques, Paul Gissen, Simon Heales, Jane A. Hurst, Richard H Scott, Emma Footitt, Sanjay Bhate, Shamima Rahman, James Davison, Stephanie Grunewald, Patrick Forny, Thomas Cullup, Spyros Batzios, Maureen Cleary, Anupam Chakrapani, and Amanda Lam

Subjects
Mitochondrial DNA, Muscle biopsy, medicine.diagnostic_test, business.industry, Mitochondrial disease, medicine.disease, Omics, Bioinformatics, Article, Neuroimaging, Cohort, Medicine, Biochemical testing, Neurology (clinical), business, Genetics (clinical), Exome sequencing
Abstract

ObjectiveWe hypothesized that novel investigative pathways are needed to decrease diagnostic odysseys in pediatric mitochondrial disease and sought to determine the utility of clinical exome sequencing in a large cohort with suspected mitochondrial disease and to explore whether any of the traditional indicators of mitochondrial disease predict a confirmed genetic diagnosis.MethodsWe investigated a cohort of 85 pediatric patients using clinical exome sequencing and compared the results with the outcome of traditional diagnostic tests, including biochemical testing of routine parameters (lactate, alanine, and proline), neuroimaging, and muscle biopsy with histology and respiratory chain enzyme activity studies.ResultsWe established a genetic diagnosis in 36.5% of the cohort and report 20 novel disease-causing variants (1 mitochondrial DNA). Counterintuitively, routine biochemical markers were more predictive of mitochondrial disease than more invasive and elaborate muscle studies.ConclusionsWe propose using biochemical markers to support the clinical suspicion of mitochondrial disease and then apply first-line clinical exome sequencing to identify a definite diagnosis. Muscle biopsy studies should only be used in clinically urgent situations or to confirm an inconclusive genetic result.Classification of EvidenceThis is a Class II diagnostic accuracy study showing that the combination of CSF and plasma biochemical tests plus neuroimaging could predict the presence or absence of exome sequencing confirmed mitochondrial disorders.

Published
2021

24. SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Author

Matteo D’Antonio, Jennifer P. Nguyen, Timothy D. Arthur, Hiroko Matsui, Agnieszka D’Antonio-Chronowska, Kelly A. Frazer, Benjamin M. Neale, Mark Daly, Andrea Ganna, Christine Stevens, Gita A. Pathak, Shea J. Andrews, Masahiro Kanai, Mattia Cordioli, Juha Karjalainen, Renato Polimanti, Matti Pirinen, Nadia Harerimana, Kumar Veerapen, Brooke Wolford, Huy Nguyen, Matthew Solomonson, Rachel G. Liao, Karolina Chwialkowska, Amy Trankiem, Mary K. Balaconis, Caroline Hayward, Anne Richmond, Archie Campbell, Marcela Morris, Chloe Fawns-Ritchie, Joseph T. Glessner, Douglas M. Shaw, Xiao Chang, Hannah Polikowski, Petty E. Lauren, Hung-Hsin Chen, Zhu Wanying, Hakon Hakonarson, David J. Porteous, Jennifer Below, Kari North, Joseph B. McCormick, Paul R.H.J. Timmers, James F. Wilson, Albert Tenesa, Kenton D’Mellow, Shona M. Kerr, Mari E.K. Niemi, Lindokuhle Nkambul, Kathrin Aprile von Hohenstaufen, Ali Sobh, Madonna M. Eltoukhy, Amr M. Yassen, Mohamed A.F. Hegazy, Kamal Okasha, Mohammed A. Eid, Hanteera S. Moahmed, Doaa Shahin, Yasser M. El-Sherbiny, Tamer A. Elhadidy, Mohamed S. Abd Elghafar, Jehan J. El-Jawhari, Attia A.S. Mohamed, Marwa H. Elnagdy, Amr Samir, Mahmoud Abdel-Aziz, Walid T. Khafaga, Walaa M. El-Lawaty, Mohamed S. Torky, Mohamed R. El-shanshory, Chiara Batini, Paul H. Lee, Nick Shrine, Alexander T. Williams, Martin D. Tobin, Anna L. Guyatt, Catherine John, Richard J. Packer, Altaf Ali, Robert C. Free, Xueyang Wang, Louise V. Wain, Edward J. Hollox, Laura D. Venn, Catherine E. Bee, Emma L. Adams, Ahmadreza Niavarani, Bahareh Sharififard, Rasoul Aliannejad, Ali Amirsavadkouhi, Zeinab Naderpour, Hengameh Ansari Tadi, Afshar Etemadi Aleagha, Saeideh Ahmadi, Seyed Behrooz Mohseni Moghaddam, Alireza Adamsara, Morteza Saeedi, Hamed Abdollahi, Abdolmajid Hosseini, Pajaree Chariyavilaskul, Monpat Chamnanphon, Thitima B. Suttichet, Vorasuk Shotelersuk, Monnat Pongpanich, Chureerat Phokaew, Wanna Chetruengchai, Watsamon Jantarabenjakul, Opass Putchareon, Pattama Torvorapanit, Thanyawee Puthanakit, Pintip Suchartlikitwong, Nattiya Hirankarn, Voraphoj Nilaratanakul, Pimpayao Sodsai, Ben M. Brumpton, Kristian Hveem, Cristen Willer, Wei Zhou, Tormod Rogne, Erik Solligard, Bjørn Olav Åsvold, Malak Abedalthagafi, Manal Alaamery, Saleh Alqahtani, Dona Baraka, Fawz Al Harthi, Ebtehal Alsolm, Leen Abu Safieh, Albandary M. Alowayn, Fatimah Alqubaishi, Amal Al Mutairi, Serghei Mangul, Abdulraheem Alshareef, Mona Sawaji, Mansour Almutairi, Nora Aljawini, Nour Albesher, Yaseen M. Arabi, Ebrahim S. Mahmoud, Amin K. Khattab, Roaa T. Halawani, Ziab Z. Alahmadey, Jehad K. Albakri, Walaa A. Felemban, Bandar A. Suliman, Rana Hasanato, Laila Al-Awdah, Jahad Alghamdi, Deema AlZahrani, Sameera AlJohani, Hani Al-Afghani, May Alrashed, Nouf AlDhawi, Hadeel AlBardis, Sarah Alkwai, Moneera Alswailm, Faisal Almalki, Maha Albeladi, Iman Almohammed, Eman Barhoush, Anoud Albader, Salam Massadeh, Abdulaziz AlMalik, Sara Alotaibi, Bader Alghamdi, Junghyun Jung, Mohammad S. Fawzy, Yunsung Lee, Per Magnus, Lill-Iren S. Trogstad, Øyvind Helgeland, Jennifer R. Harris, Massimo Mangino, Tim D. Spector, Duncan Emma, Sandra P. Smieszek, Bartlomiej P. Przychodzen, Christos Polymeropoulos, Vasilios Polymeropoulos, Mihael H. Polymeropoulos, Israel Fernandez-Cadenas, Jordi Perez-Tur, Laia Llucià-Carol, Natalia Cullell, Elena Muiño, Jara Cárcel-Márquez, Marta L. DeDiego, Lara Lloret Iglesias, Anna M. Planas, Alex Soriano, Veronica Rico, Daiana Agüero, Josep L. Bedini, Francisco Lozano, Carlos Domingo, Veronica Robles, Francisca Ruiz-Jaén, Leonardo Márquez, Juan Gomez, Eliecer Coto, Guillermo M. Albaiceta, Marta García-Clemente, David Dalmau, Maria J. Arranz, Beatriz Dietl, Alex Serra-Llovich, Pere Soler, Roger Colobrán, Andrea Martín-Nalda, Alba Parra Martínez, David Bernardo, Silvia Rojo, Aida Fiz-López, Elisa Arribas, Paloma de la Cal-Sabater, Tomás Segura, Esther González-Villa, Gemma Serrano-Heras, Joan Martí-Fàbregas, Elena Jiménez-Xarrié, Alicia de Felipe Mimbrera, Jaime Masjuan, Sebastian García-Madrona, Anna Domínguez-Mayoral, Joan Montaner Villalonga, Paloma Menéndez-Valladares, Daniel I. Chasman, Julie E. Buring, Paul M. Ridker, Giulianini Franco, Howard D. Sesso, JoAnn E. Manson, Joseph R. Glessner, Carolina Medina-Gomez, Andre G. Uitterlinden, M. Arfan Ikram, Kati Kristiansson, Sami Koskelainen, Markus Perola, Kati Donner, Katja Kivinen, Aarno Palotie, Samuli Ripatti, Sanni Ruotsalainen, Mari Kaunisto, null FinnGen, Tomoko Nakanishi, Guillaume Butler-Laporte, Vincenzo Forgetta, David R. Morrison, Biswarup Ghosh, Laetitia Laurent, Alexandre Belisle, Danielle Henry, Tala Abdullah, Olumide Adeleye, Noor Mamlouk, Nofar Kimchi, Zaman Afrasiabi, Nardin Rezk Branka Vulesevic, Meriem Bouab, Charlotte Guzman, Louis Petitjean, Chris Tselios, Xiaoqing Xue, Erwin Schurr, Jonathan Afilalo, Marc Afilalo, Maureen Oliveira, Bluma Brenner, Pierre Lepage, Jiannis Ragoussis, Daniel Auld, Nathalie Brassard, Madeleine Durand, Michaël Chassé, Daniel E. Kaufmann, G. Mark Lathrop, Vincent Mooser, J. Brent Richards, Rui Li, Darin Adra, Souad Rahmouni, Michel Georges, Michel Moutschen, Benoit Misset, Gilles Darcis, Julien Guiot, Julien Guntz, Samira Azarzar, Stéphanie Gofflot, Yves Beguin, Sabine Claassen, Olivier Malaise, Pascale Huynen, Christelle Meuris, Marie Thys, Jessica Jacques, Philippe Léonard, Frederic Frippiat, Jean-Baptiste Giot, Anne-Sophie Sauvage, Christian Von Frenckell, Yasmine Belhaj, Bernard Lambermont, Sara Pigazzini, Lindokuhle Nkambule, Michelle Daya, Jonathan Shortt, Nicholas Rafaels, Stephen J. Wicks, Kristy Crooks, Kathleen C. Barnes, Christopher R. Gignoux, Sameer Chavan, Triin Laisk, Kristi Läll, Maarja Lepamets, Reedik Mägi, Tõnu Esko, Ene Reimann, Lili Milani, Helene Alavere, Kristjan Metsalu, Mairo Puusepp, Andres Metspalu, Paul Naaber, Edward Laane, Jaana Pesukova, Pärt Peterson, Kai Kisand, Jekaterina Tabri, Raili Allos, Kati Hensen, Joel Starkopf, Inge Ringmets, Anu Tamm, Anne Kallaste, Pierre-Yves Bochud, Carlo Rivolta, Stéphanie Bibert, Mathieu Quinodoz, Dhryata Kamdar, Noémie Boillat, Semira Gonseth Nussle, Werner Albrich, Noémie Suh, Dionysios Neofytos, Véronique Erard, Cathy Voide, null FHoGID, null RegCOVID, null P-PredictUs, null SeroCOVID, null CRiPSI, Rafael de Cid, Iván Galván-Femenía, Natalia Blay, Anna Carreras, Beatriz Cortés, Xavier Farré, Lauro Sumoy, Victor Moreno, Josep Maria Mercader, Marta Guindo-Martinez, David Torrents, Manolis Kogevinas, Judith Garcia-Aymerich, Gemma Castaño-Vinyals, Carlota Dobaño, Alessandra Renieri, Francesca Mari, Chiara Fallerini, Sergio Daga, Elisa Benetti, Margherita Baldassarri, Francesca Fava, Elisa Frullanti, Floriana Valentino, Gabriella Doddato, Annarita Giliberti, Rossella Tita, Sara Amitrano, Mirella Bruttini, Susanna Croci, Ilaria Meloni, Maria Antonietta Mencarelli, Caterina Lo Rizzo, Anna Maria Pinto, Giada Beligni, Andrea Tommasi, Laura Di Sarno, Maria Palmieri, Miriam Lucia Carriero, Diana Alaverdian, Stefano Busani, Raffaele Bruno, Marco Vecchia, Mary Ann Belli, Nicola Picchiotti, Maurizio Sanarico, Marco Gori, Simone Furini, Stefania Mantovani, Serena Ludovisi, Mario Umberto Mondelli, Francesco Castelli, Eugenia Quiros-Roldan, Melania Degli Antoni, Isabella Zanella, Massimo Vaghi, Stefano Rusconi, Matteo Siano, Francesca Montagnani, Arianna Emiliozzi, Massimiliano Fabbiani, Barbara Rossetti, Elena Bargagli, Laura Bergantini, Miriana D’Alessandro, Paolo Cameli, David Bennett, Federico Anedda, Simona Marcantonio, Sabino Scolletta, Federico Franchi, Maria Antonietta Mazzei, Susanna Guerrini, Edoardo Conticini, Luca Cantarini, Bruno Frediani, Danilo Tacconi, Chiara Spertilli, Marco Feri, Alice Donati, Raffaele Scala, Luca Guidelli, Genni Spargi, Marta Corridi, Cesira Nencioni, Leonardo Croci, Maria Bandini, Gian Piero Caldarelli, Paolo Piacentini, Elena Desanctis, Silvia Cappelli, Anna Canaccini, Agnese Verzuri, Valentina Anemoli, Agostino Ognibene, Alessandro Pancrazzi, Maria Lorubbio, Antonella D’Arminio Monforte, Federica Gaia Miraglia, Massimo Girardis, Sophie Venturelli, Andrea Cossarizza, Andrea Antinori, Alessandra Vergori, Arianna Gabrieli, Agostino Riva, Daniela Francisci, Elisabetta Schiaroli, Francesco Paciosi, Pier Giorgio Scotton, Francesca Andretta, Sandro Panese, Renzo Scaggiante, Francesca Gatti, Saverio Giuseppe Parisi, Stefano Baratti, Matteo Della Monica, Carmelo Piscopo, Mario Capasso, Roberta Russo, Immacolata Andolfo, Achille Iolascon, Giuseppe Fiorentino, Massimo Carella, Marco Castori, Giuseppe Merla, Gabriella Maria Squeo, Filippo Aucella, Pamela Raggi, Carmen Marciano, Rita Perna, Matteo Bassetti, Antonio Di Biagio, Maurizio Sanguinetti, Luca Masucci, Serafina Valente, Marco Mandalà, Alessia Giorli, Lorenzo Salerni, Patrizia Zucchi, Pierpaolo Parravicini, Elisabetta Menatti, Tullio Trotta, Ferdinando Giannattasio, Gabriella Coiro, Fabio Lena, Domenico A. Coviello, Cristina Mussini, Enrico Martinelli, Sandro Mancarella, Luisa Tavecchia, Lia Crotti, Chiara Gabbi, Marco Rizzi, Franco Maggiolo, Diego Ripamonti, Tiziana Bachetti, Maria Teresa La Rovere, Simona Sarzi-Braga, Maurizio Bussotti, Stefano Ceri, Pietro Pinoli, Francesco Raimondi, Filippo Biscarini, Alessandra Stella, Kristina Zguro, Katia Capitani, Claudia Suardi, Simona Dei, Gianfranco Parati, Sabrina Ravaglia, Rosangela Artuso, Giordano Bottà, Paolo Di Domenico, Ilaria Rancan, Antonio Perrella Francesco Bianchi, Davide Romani, Paola Bergomi, Emanuele Catena, Riccardo Colombo, Marco Tanfoni, Antonella Vincenti, Claudio Ferri, Davide Grassi, Gloria Pessina, Mario Tumbarello, Massimo Di Pietro, Ravaglia Sabrina, Sauro Luchi, Chiara Barbieri, Donatella Acquilini, Elena Andreucci, Francesco Vladimiro Segala, Giusy Tiseo, Marco Falcone, Mirjam Lista, Monica Poscente, Oreste De Vivo, Paola Petrocelli, Alessandra Guarnaccia, Silvia Baroni, Albert V. Smith, Andrew P. Boughton, Kevin W. Li, Jonathon LeFaive, Aubrey Annis, Anne E. Justice, Tooraj Mirshahi, Geetha Chittoor, Navya Shilpa Josyula, Jack A. Kosmicki, Manuel A.R. Ferreira, Joseph B. Leader, Dave J. Carey, Matthew C. Gass, Julie E. Horowitz, Michael N. Cantor, Ashish Yadav, Aris Baras, Goncalo R. Abecasis, David A. van Heel, Karen A. Hunt, Dan Mason, Qin Qin Huang, Sarah Finer, null Genes & Health Research Team, Bhavi Trivedi, Christopher J. Griffiths, Hilary C. Martin, John Wright, Richard C. Trembath, Nicole Soranzo, Jing Hua Zhao, Adam S. Butterworth, John Danesh, Emanuele Di Angelantonio, Lude Franke Marike Boezen, Patrick Deelen, Annique Claringbould, Esteban Lopera, Robert Warmerdam, Judith.M. Vonk, Irene van Blokland, Pauline Lanting, Anil P.S. Ori, Brooke Wolford Sebastian Zöllner, Jiongming Wang, Andrew Beck, Gina Peloso, Yuk-Lam Ho, Yan V. Sun, Jennifer E. Huffman, Christopher J. O’Donnell, Kelly Cho, Phil Tsao, J. Michael Gaziano, Michel (M.G.) Nivard, Eco (E.J.C.) de geus, Meike Bartels, Jouke Jan Hottenga, Scott T. Weiss, Elizabeth W. Karlson, Jordan W. Smoller, Robert C. Green, Yen-Chen Anne Feng, Josep Mercader, Shawn N. Murphy, James B. Meigs, Ann E. Woolley, Emma F. Perez, Daniel Rader, Anurag Verma, Marylyn D. Ritchie, Binglan Li, Shefali S. Verma, Anastasia Lucas, Yuki Bradford, Hugo Zeberg, Robert Frithiof, Michael Hultström, Miklos Lipcsey, Lindo Nkambul, Nicolas Tardif, Olav Rooyackers, Jonathan Grip, Tomislav Maricic, Konrad J. Karczewski, Elizabeth G. Atkinson, Kristin Tsuo, Nikolas Baya, Patrick Turley, Rahul Gupta, Shawneequa Callier, Raymond K. Walters, Duncan S. Palmer, Gopal Sarma, Nathan Cheng, Wenhan Lu, Sam Bryant, Claire Churchhouse, Caroline Cusick, Jacqueline I. Goldstein, Daniel King, Cotton Seed, Hilary Finucane, Alicia R. Martin, F. Kyle Satterstrom, Daniel J. Wilson, Jacob Armstrong, Justine K. Rudkin, Gavin Band, Sarah G. Earle, Shang-Kuan Lin, Nicolas Arning, Derrick W. Crook, David H. Wyllie, Anne Marie O’Connell, Chris C.A. Spencer, Nils Koelling, Mark J. Caulfield, Richard H. Scott, Tom Fowler, Loukas Moutsianas, Athanasios Kousathanas, Dorota Pasko, Susan Walker, Augusto Rendon, Alex Stuckey, Christopher A. Odhams, Daniel Rhodes, Georgia Chan, Prabhu Arumugam, Catherine A. Ball, Eurie L. Hong, Kristin Rand, Ahna Girshick, Harendra Guturu, Asher Haug Baltzell, Genevieve Roberts, Danny Park, Marie Coignet, Shannon McCurdy, Spencer Knight, Raghavendran Partha, Brooke Rhead, Miao Zhang, Nathan Berkowitz, Michael Gaddis, Keith Noto, Luong Ruiz, Milos Pavlovic, Laura G. Sloofman, Alexander W. Charney, Noam D. Beckmann, Eric E. Schadt, Daniel M. Jordan, Ryan C. Thompson, Kyle Gettler, Noura S. Abul-Husn, Steven Ascolillo, Joseph D. Buxbaum, Kumardeep Chaudhary, Judy H. Cho, Yuval Itan, Eimear E. Kenny, Gillian M. Belbin, Stuart C. Sealfon, Robert P. Sebra, Irene Salib, Brett L. Collins, Tess Levy, Bari Britvan, Katherine Keller, Lara Tang, Michael Peruggia, Liam L. Hiester, Kristi Niblo, Alexandra Aksentijevich, Alexander Labkowsky, Avromie Karp, Menachem Zlatopolsky, Michael Preuss, Ruth J.F. Loos, Girish N. Nadkarni, Ron Do, Clive Hoggart, Sam Choi, Slayton J. Underwood, Paul O’Reilly, Laura M. Huckins, Marissa Zyndorf, AII - Infectious diseases, Amsterdam Neuroscience - Neuroinfection & -inflammation, and Neurology

Subjects
Medical Physiology, Gene Expression, Genome-wide association study, Genome, Severity of Illness Index, colocalization, Gene expression, Databases, Genetic, Ethnicity, 2.1 Biological and endogenous factors, GWAS, Aetiology, Biology (General), Lung, Genetics, Chromosome Mapping, Single Nucleotide, Organ Specificity, Biotechnology, Cell type, QH301-705.5, Quantitative Trait Loci, Single-nucleotide polymorphism, Biology, eQTL, Polymorphism, Single Nucleotide, Article, General Biochemistry, Genetics and Molecular Biology, Databases, Genetic, SNP, Humans, Genetic Predisposition to Disease, COVID-19 Host Genetics Initiative, Polymorphism, Gene, COVID-19, SARS-CoV-2, Gene Expression Profiling, Prevention, Human Genome, Computational Biology, Genetic Variation, Good Health and Well Being, Expression quantitative trait loci, Biochemistry and Cell Biology, Transcriptome, Genome-Wide Association Study
Abstract

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types., Graphical abstract, D’Antonio et al. characterize associations between GWAS signals for COVID-19 disease and eQTLs in 69 human tissues to identify causal variants and their underlying molecular mechanisms. They show that diverse symptoms and disease severity of COVID-19 are associated with variants affecting gene expression in a wide variety of tissues.

Published
2022
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25. Pathogenic huntingtin repeat expansions in patients with frontotemporal dementia and amyotrophic lateral sclerosis

Author

Ramita Dewan, Ruth Chia, Jinhui Ding, Richard A. Hickman, Thor D. Stein, Yevgeniya Abramzon, Sarah Ahmed, Marya S. Sabir, Makayla K. Portley, Arianna Tucci, Kristina Ibáñez, F.N.U. Shankaracharya, Pamela Keagle, Giacomina Rossi, Paola Caroppo, Fabrizio Tagliavini, Maria L. Waldo, Per M. Johansson, Christer F. Nilsson, James B. Rowe, Luisa Benussi, Giuliano Binetti, Roberta Ghidoni, Edwin Jabbari, Coralie Viollet, Jonathan D. Glass, Andrew B. Singleton, Vincenzo Silani, Owen A. Ross, Mina Ryten, Ali Torkamani, Toshiko Tanaka, Luigi Ferrucci, Susan M. Resnick, Stuart Pickering-Brown, Christopher B. Brady, Neil Kowal, John A. Hardy, Vivianna Van Deerlin, Jean Paul Vonsattel, Matthew B. Harms, Huw R. Morris, Raffaele Ferrari, John E. Landers, Adriano Chiò, J. Raphael Gibbs, Clifton L. Dalgard, Sonja W. Scholz, Bryan J. Traynor, Adelani Adeleye, Camille Alba, Dagmar Bacikova, Daniel N. Hupalo, Elisa McGrath Martinez, Harvey B. Pollard, Gauthaman Sukumar, Anthony R. Soltis, Meila Tuck, Xijun Zhang, Matthew D. Wilkerson, Bradley N. Smith, Nicola Ticozzi, Claudia Fallini, Athina Soragia Gkazi, Simon D. Topp, Jason Kost, Emma L. Scotter, Kevin P. Kenna, Jack W. Miller, Cinzia Tiloca, Caroline Vance, Eric W. Danielson, Claire Troakes, Claudia Colombrita, Safa Al-Sarraj, Elizabeth A. Lewis, Andrew King, Daniela Calini, Viviana Pensato, Barbara Castellotti, Jacqueline de Belleroche, Frank Baas, Anneloor L.M.A. ten Asbroek, Peter C. Sapp, Diane McKenna-Yasek, Russell L. McLaughlin, Meraida Polak, Seneshaw Asress, Jesús Esteban-Pérez, José Luis Muñoz-Blanco, Zorica Stevic, Sandra D’Alfonso, Letizia Mazzini, Giacomo P. Comi, Roberto Del Bo, Mauro Ceroni, Stella Gagliardi, Giorgia Querin, Cinzia Bertolin, Wouter van Rheenen, Frank P. Diekstra, Rosa Rademakers, Marka van Blitterswijk, Kevin B. Boylan, Giuseppe Lauria, Stefano Duga, Stefania Corti, Cristina Cereda, Lucia Corrado, Gianni Sorarù, Kelly L. Williams, Garth A. Nicholson, Ian P. Blair, Claire Leblond-Manry, Guy A. Rouleau, Orla Hardiman, Karen E. Morrison, Jan H. Veldink, Leonard H. van den Berg, Ammar Al-Chalabi, Hardev Pall, Pamela J. Shaw, Martin R. Turner, Kevin Talbot, Franco Taroni, Alberto García-Redondo, Zheyang Wu, Cinzia Gellera, Antonia Ratti, Robert H. Brown, Christopher E. Shaw, John C. Ambrose, Prabhu Arumugam, Emma L. Baple, Marta Bleda, Freya Boardman-Pretty, Jeanne M. Boissiere, Christopher R. Boustred, H. Brittain, Mark J. Caulfield, Georgia C. Chan, Clare E.H. Craig, Louise C. Daugherty, Anna de Burca, Andrew Devereau, Greg Elgar, Rebecca E. Foulger, Tom Fowler, Pedro Furió-Tarí, Joanne M. Hackett, Dina Halai, Angela Hamblin, Shirley Henderson, James E. Holman, Tim J.P. Hubbard, Rob Jackson, Louise J. Jones, Dalia Kasperaviciute, Melis Kayikci, Lea Lahnstein, Kay Lawson, Sarah E.A. Leigh, Ivonne U.S. Leong, Javier F. Lopez, Fiona Maleady-Crowe, Joanne Mason, Ellen M. McDonagh, Loukas Moutsianas, Michael Mueller, Nirupa Murugaesu, Anna C. Need, Chris A. Odhams, Christine Patch, Daniel Perez-Gil, Dimitris Polychronopoulos, John Pullinger, Tahrima Rahim, Augusto Rendon, Pablo Riesgo-Ferreiro, Tim Rogers, Kevin Savage, Kushmita Sawant, Richard H. Scott, Afshan Siddiq, Alexander Sieghart, Damian Smedley, Katherine R. Smith, Alona Sosinsky, William Spooner, Helen E. Stevens, Alexander Stuckey, Razvan Sultana, Ellen R.A. Thomas, Simon R. Thompson, Carolyn Tregidgo, Emma Walsh, Sarah A. Watters, Matthew J. Welland, Eleanor Williams, Katarzyna Witkowska, Suzanne M. Wood, Magdalena Zarowiecki, Sampath Arepalli, Pavan Auluck, Robert H. Baloh, Robert Bowser, Alexis Brice, James Broach, William Camu, John Cooper-Knock, Philippe Corcia, Carsten Drepper, Vivian E. Drory, Travis L. Dunckley, Faraz Faghri, Jennifer Farren, Eva Feldman, Mary Kay Floeter, Pietro Fratta, Glenn Gerhard, Summer B. Gibson, Stephen A. Goutman, Terry D. Heiman-Patterson, Dena G. Hernandez, Ben Hoover, Lilja Jansson, Freya Kamel, Janine Kirby, Neil W. Kowall, Hannu Laaksovirta, Francesco Landi, Isabelle Le Ber, Serge Lumbroso, Daniel JL. MacGowan, Nicholas J. Maragakis, Gabriele Mora, Kevin Mouzat, Liisa Myllykangas, Mike A. Nalls, Richard W. Orrell, Lyle W. Ostrow, Roger Pamphlett, Erik Pioro, Stefan M. Pulst, John M. Ravits, Alan E. Renton, Wim Robberecht, Ian Robey, Ekaterina Rogaeva, Jeffrey D. Rothstein, Michael Sendtner, Katie C. Sidle, Zachary Simmons, David J. Stone, Pentti J. Tienari, John Q. Trojanowski, Juan C. Troncoso, Miko Valori, Philip Van Damme, Ludo Van Den Bosch, Lorne Zinman, Diego Albani, Barbara Borroni, Alessandro Padovani, Amalia Bruni, Jordi Clarimon, Oriol Dols-Icardo, Ignacio Illán-Gala, Alberto Lleó, Adrian Danek, Daniela Galimberti, Elio Scarpini, Maria Serpente, Caroline Graff, Huei-Hsin Chiang, Behzad Khoshnood, Linn Öijerstedt, Christopher M. Morris, Benedetta Nacmias, Sandro Sorbi, Jorgen E. Nielsen, Lynne E. Hjermind, Valeria Novelli, Annibale A. Puca, Pau Pastor, Ignacio Alvarez, Monica Diez-Fairen, Miquel Aguilar, Robert Perneczky, Janine Diehl-Schimd, Mina Rossi, Agustin Ruiz, Mercè Boada, Isabel Hernández, Sonia Moreno-Grau, Johannes C. Schlachetzki, Dag Aarsland, Marilyn S. Albert, Johannes Attems, Matthew J. Barrett, Thomas G. Beach, Lynn M. Bekris, David A. Bennett, Lilah M. Besser, Eileen H. Bigio, Sandra E. Black, Bradley F. Boeve, Ryan C. Bohannan, Francesca Brett, Maura Brunetti, Chad A. Caraway, Jose-Alberto Palma, Andrea Calvo, Antonio Canosa, Dennis Dickson, Charles Duyckaerts, Kelley Faber, Tanis Ferman, Margaret E. Flanagan, Gianluca Floris, Tatiana M. Foroud, Juan Fortea, Ziv Gan-Or, Steve Gentleman, Bernardino Ghetti, Jesse Raphael Gibbs, Alison Goate, David Goldstein, Isabel González-Aramburu, Neill R. Graff-Radford, Angela K. Hodges, Heng-Chen Hu, Daniel Hupalo, Jon Infante, Alex Iranzo, Scott M. Kaiser, Horacio Kaufmann, Julia Keith, Ronald C. Kim, Gregory Klein, Rejko Krüger, Walter Kukull, Amanda Kuzma, Carmen Lage, Suzanne Lesage, James B. Leverenz, Giancarlo Logroscino, Grisel Lopez, Seth Love, Qinwen Mao, Maria Jose Marti, Elisa Martinez-McGrath, Mario Masellis, Eliezer Masliah, Patrick May, Ian McKeith, Marek-Marsel Mesulam, Edwin S. Monuki, Kathy L. Newell, Lucy Norcliffe-Kaufmann, Laura Palmer, Matthew Perkins, Olga Pletnikova, Laura Molina-Porcel, Regina H. Reynolds, Eloy Rodríguez-Rodríguez, Jonathan D. Rohrer, Pascual Sanchez-Juan, Clemens R. Scherzer, Geidy E. Serrano, Vikram Shakkottai, Ellen Sidransky, Nahid Tayebi, Alan J. Thomas, Bension S. Tilley, Ronald L. Walton, Randy Woltjer, Zbigniew K. Wszolek, Georgia Xiromerisiou, Chiara Zecca, Hemali Phatnani, Justin Kwan, Dhruv Sareen, James R. Broach, Ximena Arcila-Londono, Edward B. Lee, Neil A. Shneider, Ernest Fraenkel, Noah Zaitlen, James D. Berry, Andrea Malaspina, Gregory A. Cox, Leslie M. Thompson, Steve Finkbeiner, Efthimios Dardiotis, Timothy M. Miller, Siddharthan Chandran, Suvankar Pal, Eran Hornstein, Daniel J. MacGowan, Terry Heiman-Patterson, Molly G. Hammell, Nikolaos.A. Patsopoulos, Oleg Butovsky, Joshua Dubnau, Avindra Nath, Matt Harms, Eleonora Aronica, Mary Poss, Jennifer Phillips-Cremins, John Crary, Nazem Atassi, Dale J. Lange, Darius J. Adams, Leonidas Stefanis, Marc Gotkine, Suma Babu, Towfique Raj, Sabrina Paganoni, Ophir Shalem, Colin Smith, Bin Zhang, Brent Harris, Iris Broce, Vivian Drory, John Ravits, Corey McMillan, Vilas Menon, Lani Wu, Steven Altschuler, Khaled Amar, Neil Archibald, Oliver Bandmann, Erica Capps, Alistair Church, Jan Coebergh, Alyssa Costantini, Peter Critchley, Boyd CP. Ghosh, Michele T.M. Hu, Christopher Kobylecki, P. Nigel Leigh, Carl Mann, Luke A. Massey, Uma Nath, Nicola Pavese, Dominic Paviour, Jagdish Sharma, Jenny Vaughan, HUS Neurocenter, Neurologian yksikkö, Department of Neurosciences, Clinicum, Pentti Tienari / Principal Investigator, Parkinson's UK, Human Genetics, ARD - Amsterdam Reproduction and Development, ANS - Complex Trait Genetics, Pathology, ANS - Cellular & Molecular Mechanisms, AII - Inflammatory diseases, Universidad de Cantabria, Rowe, James [0000-0001-7216-8679], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Huntington's Disease, Pathology, amyotrophic lateral sclerosis, Huntingtin, Neurology, 1702 Cognitive Sciences, International ALS/FTD Genomics Consortium, Neurodegenerative, frontotemporal dementia, 3124 Neurology and psychiatry, 0302 clinical medicine, Medicine, 2.1 Biological and endogenous factors, Psychology, Amyotrophic lateral sclerosis, Aetiology, Alzheimer's Disease Related Dementias (ADRD), NYGC ALS Consortium, Huntingtin Protein, DNA Repeat Expansion, General Neuroscience, Frontotemporal Dementia (FTD), International FTD Genetics Consortium, whole-genome sequencing, Frontotemporal Dementia, Neurological, Cognitive Sciences, Lewy body dementia, huntingtin, repeat expansions, Amyotrophic Lateral Sclerosis, Humans, Mutation, Whole Genome Sequencing, Frontotemporal dementia, Huntington’s disease, medicine.medical_specialty, congenital, hereditary, and neonatal diseases and abnormalities, FALS Sequencing Consortium, Article, 03 medical and health sciences, Atrophy, Rare Diseases, American Genome Center, Clinical Research, mental disorders, Genetics, Acquired Cognitive Impairment, Dementia, PROSPECT Consortium, Neurology & Neurosurgery, Lewy body, business.industry, International LBD Genomics Consortium, Neurosciences, 3112 Neurosciences, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), nutritional and metabolic diseases, medicine.disease, Brain Disorders, nervous system diseases, 030104 developmental biology, Genomics England Research Consortium, 1701 Psychology, ALS, business, 1109 Neurosciences, 030217 neurology & neurosurgery
Abstract

Hannu Laaksovirta konsortion jäsenenä. The Genomics England Research Consortium, The International ALS/FTD Genomics Consortium (iAFGC), The International FTD Genetics Consortium (IFGC), The International LBD Genomics Consortium (iLBDGC), The NYGC ALS Consortium, The PROSPECT Consortium,17 James B. Rowe,17 Luisa Benussi,18 Giuliano Binetti,18,19 Roberta Ghidoni,18 Edwin Jabbari,20,21 Coralie Viollet,22 Jonathan D. Glass,23 Andrew B. Singleton,24 Vincenzo Silani,25,26 Owen A. Ross,27 Mina Ryten,8,28,29 Ali Torkamani,30 Toshiko Tanaka,31 Luigi Ferrucci,31 Susan M. Resnick,32 We examined the role of repeat expansions in the pathogenesis of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) by analyzing whole-genome sequence data from 2,442 FTD/ALS patients, 2,599 Lewy body dementia (LBD) patients, and 3,158 neurologically healthy subjects. Pathogenic expansions (range, 40?64 CAG repeats) in the huntingtin (HTT) gene were found in three (0.12%) patients diagnosed with pure FTD/ALS syndromes but were not present in the LBD or healthy cohorts. We replicated our findings in an independent collection of 3,674 FTD/ALS patients. Postmortem evaluations of two patients revealed the classical TDP-43 pathology of FTD/ALS, as well as huntingtin-positive, ubiquitin-positive aggregates in the frontal cortex. The neostriatal atrophy that pathologically defines Huntington?s disease was absent in both cases. Our findings reveal an etiological relationship between HTT repeat expansions and FTD/ALS syndromes and indicate that genetic screening of FTD/ALS patients for HTT repeat expansions should be considered. We examined the role of repeat expansions in the pathogenesis of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) by analyzing whole-genome sequence data from 2,442 FTD/ALS patients, 2,599 Lewy body dementia (LBD) patients, and 3,158 neurologically healthy subjects. Pathogenic expansions (range, 40?64 CAG repeats) in the huntingtin (HTT) gene were found in three (0.12%) patients diagnosed with pure FTD/ALS syndromes but were not present in the LBD or healthy cohorts. We replicated our findings in an independent collection of 3,674 FTD/ALS patients. Postmortem evaluations of two patients revealed the classical TDP-43 pathology of FTD/ALS, as well as huntingtin-positive, ubiquitin-positive aggregates in the frontal cortex. The neostriatal atrophy that pathologically defines Huntington?s disease was absent in both cases. Our findings reveal an etiological relationship between HTT repeat expansions and FTD/ALS syndromes and indicate that genetic screening of FTD/ALS patients for HTT repeat expansions should be considered.

Published
2020
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26. Whole genome sequencing for diagnosis of neurological repeat expansion disorders

Author

Greenhalgh L, Fowler T, Karen Temple, Kane Smith, Deshpande, Subramanian S. Ajay, Bourn D, Menzies L, James M. Polke, Pasko D, Polychronopoulos D, Augusto Rendon, Pietro Fratta, Madeleine Reilly, Daugherty L, Chitty Ls, Eggleton K, Raymond Fl, Thomas T. Warner, Paul Brennan, Sian Ellard, Denise L. Perry, Jill Davison, A. C. Need, Arianna Tucci, Prasad Korlipara Lv, Mark J. Caulfield, Meriel McEntagart, Huw R. Morris, Kikkeri N. Naresh, Jenny C. Taylor, Patrick F. Chinnery, Anette Schrag, Aditi Chawla, Deans Zc, Henry Houlden, Twiss P, Douglas A, Sheikh I, Jonathan M. Schott, Hill S, Moutsianas L, Nicholas W. Wood, Tanner Hagelstrom, Robinson R, D. Kasperaviciute, Faravelli F, Rajan, Kristina Ibáñez, Antonio Rueda Martin, Emma L. Baple, Robin Howard, Ellen M. McDonagh, Elisabeth Rosser, Oprych K, Richard Festenstein, John A. Sayer, Kailash P. Bhatia, Michael A. Eberle, Andrew D Mumford, Angus-Leppan H, Thomas E, Matilde Laura, McMullan D, Brittain H, Paola Giunti, Richard H. Scott, Wilson G, Taylor Tavares Al, Ryan J. Taft, Patch C, Hyder Z, Robyn Labrum, Almheiri G, Frances Flinter, Egor Dolzhenko, Santos L, Abbs S, William G. Newman, and Jana Vandrovcova

Subjects
Whole genome sequencing, Pediatrics, medicine.medical_specialty, medicine.diagnostic_test, business.industry, Genome, Medicine, Social care, False positive rate, Allele, Family history, business, Trinucleotide repeat expansion, Genetic testing
Abstract

BackgroundRepeat expansion (RE) disorders affect ~1 in 3000 individuals and are clinically heterogeneous diseases caused by expansions of short tandem DNA repeats. Genetic testing is often locus-specific, resulting in under diagnosis of atypical clinical presentations, especially in paediatric patients without a prior positive family history. Whole genome sequencing (WGS) is emerging as a first-line test for rare genetic disorders, but until recently REs were thought to be undetectable by this approach.MethodsWGS pipelines for RE disorder detection were deployed by the 100,000 Genomes Project and Illumina Clinical Services Laboratory. Performance was retrospectively assessed across the 13 most common neurological RE loci using 793 samples with prior orthogonal testing (182 with expanded alleles and 611 with alleles within normal size) and prospectively interrogated in 13,331 patients with suspected genetic neurological disorders.FindingsWGS RE detection showed minimum 97·3% sensitivity and 99·6% specificity across all 13 disease-associated loci. Applying the pipeline to patients from the 100,000 Genomes Project identified pathogenic repeat expansions which were confirmed in 69 patients, including seven paediatric patients with no reported family history of RE disorders, with a 0.09% false positive rate.InterpretationWe show here for the first time that WGS enables the detection of causative repeat expansions with high sensitivity and specificity, and that it can be used to resolve previously undiagnosed neurological disorders. This includes children with no prior suspicion of a RE disorder. These findings are leading to diagnostic implementation of this analytical pipeline in the NHS Genomic Medicine Centres in England.FundingMedical Research Council, Department of Health and Social Care, National Health Service England, National Institute for Health Research, Illumina Inc

Published
2020
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27. A catalog of associations between rare coding variants and COVID-19 outcomes

Author

Anurag Verma, Anne E. Justice, Guillaume Butler-Laporte, E. N. Smith, Lukas Habegger, Joelle Mbatchou, Susan P. Walker, Albert Tenesa, Joseph D. Szustakowski, Konrad Rawlik, Dylan Sun, Loukas Moutsianas, Shane McCarthy, Richard H Scott, Aris Baras, Evan Maxwell, Aldo Cordova-Palomera, Tooraj Mirshahi, Dorota Pasko, David J. Carey, Sahar Esmaeli, Adam J. Mansfield, Quanli Wang, Jeffrey S. Reid, Nilanjana Banerjee, Joshua D. Backman, Athanasios Kousathanas, Ashish Yadav, Mark J. Caulfield, Alison M. Meynert, Rouel Lanche, Jack A. Kosmicki, James F. Wilson, J. Brent Richards, Heiko Runz, Gonçalo R. Abecasis, Adam E. Locke, Justin W. Davis, Mark Lathrop, Alan R. Shuldiner, Lauren Gurski, J Kenneth Baillie, Michael N. Cantor, David Goldstein, John D. Overton, Kyoko Watanabe, Amanda O'Neill, Yunfeng Huang, Jonathan Marchini, Xiaodong Bai, Krzysztof Kiryluk, Slavé Petrovski, Sean O'Keeffe, Erika Kvikstad, Anthony Marcketta, Margaret M. Parker, Giorgio Sirugo, Julie E. Horowitz, Emily Wong, Olympe Chazara, Paul Nioi, Manuel A. R. Ferreira, Sándor Szalma, Joseph B. Leader, Shareef Khalid, William J Salerno, Deepika Sharma, Tomoko Nakanishi, Marcus B. Jones, Gundula Povysil, Marylyn D. Ritchie, Colm O'Dushlaine, Xiuwen Zheng, Daniel J. Rader, Suganthi Balasubramanian, Hyun Min Kang, Yi-Pin Lai, Alexander H. Li, Xing Chen, and Erola Pairo-Castineira

Subjects
Coronavirus disease 2019 (COVID-19), business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Genome-wide association study, medicine.disease_cause, Biobank, Article, Genetic association analysis, Immunology, Multiple comparisons problem, Medicine, business, Gene, Coronavirus
Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19), a respiratory illness that can result in hospitalization or death. We investigated associations between rare genetic variants and seven COVID-19 outcomes in 543,213 individuals, including 8,248 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome-wide or when specifically focusing on (i) 14 interferon pathway genes in which rare deleterious variants have been reported in severe COVID-19 patients; (ii) 167 genes located in COVID-19 GWAS risk loci; or (iii) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, with results publicly browsable athttps://rgc-covid19.regeneron.com.

Published
2020
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28. Comparison of in silico strategies to prioritize rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders

Author

Augusto Rendon, A. Kousathanas, S. E. A. Leigh, D. Kasperaviciute, R. Jackson, J. Pullinger, Richard H. Scott, T. Rahim, Graeme C.M. Black, C. A. Odhams, Simon C Ramsden, A. Siddiq, L. Lahnstein, S. R. Thompson, Huw B. Thomas, Jenny Lord, M. Bleda, M. J. Welland, L. Moutsianas, A. Giess, Jill Clayton-Smith, A. Stuckey, Panagiotis I. Sergouniotis, H. Brittain, K. Sawant, Arianna Tucci, A. Sosinsky, I. U. S. Leong, Nicole Gossan, William G. Newman, Christopher Campbell, Mark J. Caulfield, T. Rogers, Diana Baralle, Andrew G. L. Douglas, A. L. Taylor Tavares, N. Murugaesu, Gavin Arno, S. M. Wood, Louise J. Jones, Robert A. Hirst, Htoo A Wai, A. Hamblin, Glenda M. Beaman, P. O’Donovan, A. Sieghart, F. Maleady-Crowe, S. Henderson, M. Tanguy, Claire Hardcastle, C. R. Boustred, G. C. Chan, M. McEntagart, Beatriz Gomes-Silva, E. Williams, Andrew R. Webster, Ellen R A Thomas, T. Fowler, Christine Patch, Raymond T. O'Keefe, Elizabeth A. Jones, D. Perez-Gil, M. B. Pereira, R. Bevers, F. J. Lopez, Jamie M Ellingford, Kevin Webb, M. Kayikci, S. C. Smith, F. Boardman-Pretty, Charlie Rowlands, K. Witkowsa, P. Arumugam, A. C. Need, Tim Hubbard, J. C. Ambrose, M. Mueller, Christopher O'Callaghan, F. Minneci, and K. Savage

Subjects
Prioritization, Genetic testing, Science, RNA Splicing, In silico, Computational biology, Biology, Article, Diagnosis, Differential, Human disease, Databases, Genetic, Diagnosis, RNA Precursors, Genetics, Humans, Disease, Clinical genetics, Medical diagnosis, Uncertain significance, Diagnostic Techniques and Procedures, Multidisciplinary, Disease genetics, Computational Biology, Genetic Variation, Diagnostic test, Exons, Genomics, Pathogenicity, Mutation, RNA splicing, Medicine, RNA Splice Sites, Algorithms
Abstract

The development of computational methods to assess pathogenicity of pre-messenger RNA splicing variants is critical for diagnosis of human disease. We assessed the capability of eight algorithms, and a consensus approach, to prioritize 250 variants of uncertain significance (VUSs) that underwent splicing functional analyses. It is the capability of algorithms to differentiate VUSs away from the immediate splice site as being ‘pathogenic’ or ‘benign’ that is likely to have the most substantial impact on diagnostic testing. We show that SpliceAI is the best single strategy in this regard, but that combined usage of tools using a weighted approach can increase accuracy further. We incorporated prioritization strategies alongside diagnostic testing for rare disorders. We show that 15% of 2783 referred individuals carry rare variants expected to impact splicing that were not initially identified as ‘pathogenic’ or ‘likely pathogenic’; 1 in 5 of these cases could lead to new or refined diagnoses.

Published
2020
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29. Genetic mechanisms of critical illness in Covid-19

Author

Lee Murphy, Chris P. Ponting, Xia Shen, Veronique Vitart, Seán Keating, Charles J. Hinds, Kathy Rowan, James F. Wilson, Mark J. Caulfield, Caroline Hayward, Alistair Nichol, Wilna Oosthuyzen, Hugh Montgomery, David M. Maslove, Manu Shankar-Hari, Barbara Shih, Konrad Rawlik, Julian C. Knight, J Kenneth Baillie, Nicola Wrobel, Graeme R. Grimes, Chris Haley, Peter J. M. Openshaw, Loukas Moutsianas, Charlotte Summers, Angie Fawkes, David J. Porteous, Susan P. Walker, Peter Horby, Fiona Griffiths, Clark D Russell, Sara Clohisey, Marie Zechner, Anne Richmond, Timothy S. Walsh, Alison M. Meynert, Chenqing Zheng, Albert Tenesa, Bo Wang, Andy Law, Daniel F. McAuley, Andrew D. Bretherick, Max Head Fourman, Elvina Gountouna, James J Furniss, Lucija Klaric, Erola Pairo-Castineira, Malcolm G Semple, Paul Klenerman, Nicholas J. Parkinson, Lance Turtle, Richard H Scott, Dorota Pasko, Zhijian Yang, Antonia Ho, Lowell Ling, and Ranran Zhai

Subjects
business.industry, Intensive care, Genetic variation, medicine, Population study, Locus (genetics), Genome-wide association study, Disease, Bioinformatics, medicine.disease, business, Gene, Comorbidity
Abstract

The subset of patients who develop critical illness in Covid-19 have extensive inflammation affecting the lungs1 and are strikingly different from other patients: immunosuppressive therapy benefits critically-ill patients, but may harm some non-critical cases.2 Since susceptibility to life-threatening infections and immune-mediated diseases are both strongly heritable traits, we reasoned that host genetic variation may identify mechanistic targets for therapeutic development in Covid-19.3GenOMICC (Genetics Of Mortality In Critical Care, genomicc.org) is a global collaborative study to understand the genetic basis of critical illness. Here we report the results of a genome-wide association study (GWAS) in 2244 critically-ill Covid-19 patients from 208 UK intensive care units (ICUs), representing >95% of all ICU beds. Ancestry-matched controls were drawn from the UK Biobank population study and results were confirmed in GWAS comparisons with two other population control groups: the 100,000 genomes project and Generation Scotland.We identify and replicate three novel genome-wide significant associations, at chr19p13.3 (rs2109069, p = 3.98 × 10−12), within the gene encoding dipeptidyl peptidase 9 (DPP9), at chr12q24.13 (rs10735079, p =1.65 × 10−8) in a gene cluster encoding antiviral restriction enzyme activators (OAS1, OAS2, OAS3), and at chr21q22.1 (rs2236757, p = 4.99 × 10−8) in the interferon receptor gene IFNAR2. Consistent with our focus on extreme disease in younger patients with less comorbidity, we detect a stronger signal at the known 3p21.31 locus than previous studies (rs73064425, p = 4.77 × 10−30).We identify potential targets for repurposing of licensed medications. Using Mendelian randomisation we found evidence in support of a causal link from low expression of IFNAR2, and high expression of TYK2, to life-threatening disease. Transcriptome-wide association in lung tissue revealed that high expression of the monocyte/macrophage chemotactic receptor CCR2 is associated with severe Covid-19.Our results identify robust genetic signals relating to key host antiviral defence mechanisms, and mediators of inflammatory organ damage in Covid-19. Both mechanisms may be amenable to targeted treatment with existing drugs. Large-scale randomised clinical trials will be essential before any change to clinical practice.

Published
2020
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30. De novo SOX6 variants cause a neurodevelopmental syndrome associated with ADHD, craniosynostosis, and osteochondromas

Author

M. Zarowiecki, A. Devereau, S.M. Wood, J. M. Boissiere, G. Elgar, Cara Forster, Liesbeth Keldermans, A. Sieghart, Allyn McConkie-Rosell, Augusto Rendon, S. R. Thompson, D. Polychronopoulos, Alexandre Arkader, Julien Thevenon, D. Kasperaviciute, Alma Kuechler, Bryan L. Krock, Dominique Martin-Coignard, Damian Smedley, T. Rahim, Barbara Mikat, Amber Begtrup, Priya Prasad, Lindsay B. Henderson, A. Stuckey, Mathilde Nizon, Tim Hubbard, I. U. S. Leong, M. Bleda, L. Lahnstein, C. E. H. Craig, Bertrand Isidor, Sarah Leigh, Joanne Mason, L. Moutsianas, T. Fowler, A. Siddiq, J. Pullinger, Marco Angelozzi, J. Ambrose, S. A. Watters, Saadet Mercimek-Andrews, K. Lawson, Claudia A. L. Ruivenkamp, Ian D. Krantz, J. E. Holman, Solveig Heide, Christel Depienne, Elizabeth T. DeChene, L. C. Daugherty, Alvaro Serrano Russi, Arianna Tucci, Mark J. Caulfield, Marie T. McDonald, Boris Keren, A. C. Need, Damara Ortiz, Nicola Foulds, William Spooner, Dara Tolchin, Eduardo Calpena, C. R. Boustred, Abdul Haseeb, Rudolf Gorazd, Charles Coutton, Alona Sosinsky, D. Perez-Gil, Sarah Stewart, J. M. Hackett, Giada Melistaccio, Andrew O.M. Wilkie, Radka Stoeva, Cédric Le Caignec, Pauline Le Tanno, Benjamin Cogné, Martina Mueller, Naghmeh Dorrani, Pedro Furió-Tarí, Gijs W. E. Santen, Hermann-Josef Lüdecke, Jessica P. Yeager, Julian A. Martinez-Agosto, Damien Haye, Kieran B. Pechter, Mohnish Suri, Livija Medne, M. J. Welland, Patrick Reed, K. Savage, G. C. Chan, Anne C.H. Tsai, F. Maleady-Crowe, A. de Burca, Ellen M. McDonagh, T. Rogers, F. Boardman-Pretty, Emily Lancaster, Katherine R. Smith, Christopher A. Odhams, Véronique Lefebvre, M. Ryten, Olivier Pichon, D. Halai, Aleš Maver, Christine Patch, R. E. Foulger, Frédéric Bilan, Helen Stevens, Hilde Van Esch, Eleanor Williams, Brigitte Gilbert-Dussardier, C. Tregidgo, K. Witkowska, F. J. Lopez, Gwenaël Le Guyader, Richard H Scott, M. Kayikci, Ellen Thomas, and E. Walsh

Subjects
0301 basic medicine, Male, Osteochondroma, Adolescent, Transcription, Genetic, media_common.quotation_subject, Nonsense, Medizin, Active Transport, Cell Nucleus, Mutation, Missense, Biology, Cell fate determination, Translocation, Genetic, Article, Craniosynostosis, 03 medical and health sciences, Craniosynostoses, 0302 clinical medicine, Intellectual disability, Genetics, medicine, Missense mutation, Humans, Computer Simulation, Amino Acid Sequence, RNA-Seq, Child, Gene, Genetics (clinical), media_common, Base Sequence, Brain, Infant, Syndrome, medicine.disease, 030104 developmental biology, Attention Deficit Disorder with Hyperactivity, Neurodevelopmental Disorders, Child, Preschool, Genomic Structural Variation, Autism, Female, Haploinsufficiency, Transcriptome, SOXD Transcription Factors, 030217 neurology & neurosurgery
Abstract

SOX6 belongs to a family of 20 SRY-related HMG-box-containing (SOX) genes that encode transcription factors controlling cell fate and differentiation in many developmental and adult processes. For SOX6, these processes include, but are not limited to, neurogenesis and skeletogenesis. Variants in half of the SOX genes have been shown to cause severe developmental and adult syndromes, referred to as SOXopathies. We here provide evidence that SOX6 variants also cause a SOXopathy. Using clinical and genetic data, we identify 19 individuals harboring various types of SOX6 alterations and exhibiting developmental delay and/or intellectual disability; the individuals are from 17 unrelated families. Additional, inconstant features include attention-deficit/hyperactivity disorder (ADHD), autism, mild facial dysmorphism, craniosynostosis, and multiple osteochondromas. All variants are heterozygous. Fourteen are de novo, one is inherited from a mosaic father, and four offspring from two families have a paternally inherited variant. Intragenic microdeletions, balanced structural rearrangements, frameshifts, and nonsense variants are predicted to inactivate the SOX6 variant allele. Four missense variants occur in residues and protein regions highly conserved evolutionarily. These variants are not detected in the gnomAD control cohort, and the amino acid substitutions are predicted to be damaging. Two of these variants are located in the HMG domain and abolish SOX6 transcriptional activity in vitro. No clear genotype-phenotype correlations are found. Taken together, these findings concur that SOX6 haploinsufficiency leads to a neurodevelopmental SOXopathy that often includes ADHD and abnormal skeletal and other features.

Published
2020

31. Novel GDF2 Loss of Function Variant in a Family with HHT and PAVMs Expands the Phenotype Associated with BMP9 Dysfunction

Author

Respirato, T. Fowler, R. Slade, Mark J. Caulfield, K. Kerr, A. Devereau, G. Thomas, Ellen Thomas, Richard H. Scott, S Xiao, Amy Jayne McKnight, S. Balachandar, M. Mohammed, Jill Kilner, T. Graves, Ellen M. McDonagh, Claire L. Shovlin, Shane McKee, V. Mcconnell, T Ferguson, M. Sroya, F. Boardman-Pretty, Mary Alikian, A. Shimonty, Ewfw Alton, M. Aldred, Julian Redhead, and E. Curetean

Subjects
Cancer research, GDF2, Biology, Phenotype, Loss function
Published
2020
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32. Genomic medicine: time for health-care transformation

Author

Tom Fowler, Richard H Scott, and Mark J. Caulfield

Subjects
business.industry, MEDLINE, Genomics, General Medicine, Computational biology, Transformation (music), Translational Research, Biomedical, Early Diagnosis, Health care, Humans, Genomic medicine, Medicine, Precision Medicine, business
Published
2019
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33. S66 Delivering the 100,000 genomes project to establish the functional role of DNA sequence variants in respiratory rare diseases

Author

S Hasan, Ewfw Alton, Ellen M. McDonagh, Stefan J. Marciniak, Era Thomas, F. Boardman-Pretty, W. Cookson, A De Soyza, Gisli Jenkins, T. Fowler, Richard H. Scott, Deborah J. Morris-Rosendahl, S Xiao, Claire L. Shovlin, M Lovett, Claire Hogg, M Alikian, A. Devereau, F Copeland, R. Slade, Mark J. Caulfield, Miriam F. Moffatt, and D Brown

Subjects
Whole genome sequencing, business.industry, Genomics, Disease, Computational biology, medicine.disease, Genome, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, 030228 respiratory system, Tier 2 network, Human Phenotype Ontology, Medicine, 030212 general & internal medicine, business, Primary ciliary dyskinesia
Abstract

Background and aims Between July 2016 and September 2018, NHS Genomic Medicine Centres (GMCs) recruited families with specified rare diseases to the 100,000 Genomes Project for whole genome sequencing (WGS), and linkage to phenotypic information from NHS Health Records. Methods Genomics England protocols were followed for disease nominations, data model generation based on human phenotype ontology (HPO) terms,1 and development/review of PanelApp gene panels.2 Genomics England performed all WGS, data alignments, and initial variant tiering. This incorporated appropriate familial segregation patterns for variants in genes known to cause the patient‘s disease (Tier 1: clear loss of function variants, Tier2: other variants), and clear loss of function or de novo variants in other genes (Tier 3). The Respiratory GeCIP (Clinical Interpretation Partnership) was established to analyse full WGS/phenotypic datasets. Results Six respiratory diseases were nominated and passed through 100K pipelines: primary ciliary dyskinesia (PCD), familial pulmonary fibrosis (FPF), aggressive non-CF bronchiectasis, pulmonary arteriovenous malformations (PAVMs), hereditary haemorrhagic telangiectasia (HHT) and familial pneumothorax. National and international networks were established for each, including a focus on patient/public engagement. Patient results were returned to UK GMCs from August 2017. Recruited participants with recessive and dominant diseases each had 0–2 Tier 1 variants, 0–2 Tier 2 variants and up to 536 Tier 3 variants. Genomic diagnoses have been fed back to 57 respiratory families for 15 different genes in PCD, FPF, non-CF bronchiectasis, and PAVMs/HHT, already modifying PanelApp, with validations in two potentially new ciliopathy genes in progress. Full WGS results have been released quarterly to the Research Data Embassy at steadily increasing numbers. HPO term capture identifies further patients; for example, there are data on 269 families recruited with bronchiectasis plus another 27 with relevant HPO terms. Respiratory GeCIP Data Embassy access and Projects were secured through 2018–2019. New analytic resources available through the Data Embassy (particularly LabKey and IVA 2.0) enable >90 Domain members to identify annotated variants through indexed systems. Custom scripts are being used to access variant information from the whole genome. Conclusions The Respiratory GeCIP has established a collaborative resource for the advancement of NHS Respiratory Genomics. References http://human-phenotype-ontology.github.io/ https://bioinfo.extge.co.uk/crowdsourcing/PanelApp

Published
2019
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34. PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels

Author

Antonio Rueda, Martin, Eleanor, Williams, Rebecca E, Foulger, Sarah, Leigh, Louise C, Daugherty, Olivia, Niblock, Ivone U S, Leong, Katherine R, Smith, Oleg, Gerasimenko, Eik, Haraldsdottir, Ellen, Thomas, Richard H, Scott, Emma, Baple, Arianna, Tucci, Helen, Brittain, Anna, de Burca, Kristina, Ibañez, Dalia, Kasperaviciute, Damian, Smedley, Mark, Caulfield, Augusto, Rendon, and Ellen M, McDonagh

Subjects
Genetic Markers, Consensus, Rare Diseases, England, Computational Biology, Crowdsourcing, High-Throughput Nucleotide Sequencing, Humans, Genetic Testing, Expert Testimony, Software
Published
2019

35. 69 Looking beyond no primary findings in the 100,000 genomes project: can additional bioinformatics analysis reveal diagnoses?

Author

Jane A. Hurst, Emma Clement, Richard H Scott, Emma Ashton, F Faravelli, Eleanor Hay, Deborah Morrogh, Lyn S. Chitty, Patrick Lombard, Ajith Kumar, and Andrew Buckton

Subjects
Whole genome sequencing, Genetic heterogeneity, business.industry, Mutation (genetic algorithm), Epidermolysis bullosa dystrophica, Medicine, Identification (biology), Computational biology, business, medicine.disease, Genome, Penetrance, Rare disease
Abstract

Rare diseases, particularly those with great phenotypic and genetic heterogeneity, remain a diagnostic challenge. Broadening the investigative approach through whole genome sequencing (WGS) is anticipated to improve diagnostic yield. Despite this, substantial numbers of patients remain undiagnosed through current 100,000 Genomes Project pipelines. In these cases, the causative mutation may not be prioritised due to lack of evidence associating the gene with a specific phenotype, or as a result of being inadvertently filtered out. A systematic approach to additional data analysis utilising both inheritance model filtering and ranking algorithm tools has been piloted in cases with no primary findings (NPF). Examples of diagnoses secured include a de novo TAB2mutation, causing a connective tissue phenotype with congenital heart disease and a paternally inherited COL7A1mutation, causing a variable penetrance skin blistering disorder, epidermolysis bullosa dystrophica. Identification of causative variants in WGS data remains challenging. Data led approaches to optimising additional review of cases with NPF have the prospect of improving both sensitivity and cost efficiency and may provide earlier diagnosis for individuals with rare disease, ending their diagnostic odyssey. Establishing a standardised approach to reanalysis will be particularly important as we approach the introduction of an NHS clinical sequencing service.

Published
2019
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36. Prenatal exome sequencing analysis in fetal structural anomalies detected by ultrasonography (PAGE): a cohort study

Author

Jenny, Lord, Dominic J, McMullan, Ruth Y, Eberhardt, Gabriele, Rinck, Susan J, Hamilton, Elizabeth, Quinlan-Jones, Elena, Prigmore, Rebecca, Keelagher, Sunayna K, Best, Georgina K, Carey, Rhiannon, Mellis, Sarah, Robart, Ian R, Berry, Kate E, Chandler, Deirdre, Cilliers, Lara, Cresswell, Sandra L, Edwards, Carol, Gardiner, Alex, Henderson, Simon T, Holden, Tessa, Homfray, Tracy, Lester, Rebecca A, Lewis, Ruth, Newbury-Ecob, Katrina, Prescott, Oliver W, Quarrell, Simon C, Ramsden, Eileen, Roberts, Dagmar, Tapon, Madeleine J, Tooley, Pradeep C, Vasudevan, Astrid P, Weber, Diana G, Wellesley, Paul, Westwood, Helen, White, Michael, Parker, Denise, Williams, Lucy, Jenkins, Richard H, Scott, Mark D, Kilby, Lyn S, Chitty, Matthew E, Hurles, Eamonn R, Maher, and Elizabeth, Wilson

Subjects
Male, Parents, medicine.medical_specialty, DNA Copy Number Variations, Perinatal Death, Abnormal Karyotype, Aneuploidy, Article, Congenital Abnormalities, Fetal Development, 03 medical and health sciences, Fetus, 0302 clinical medicine, Pregnancy, Prenatal Diagnosis, Exome Sequencing, Correspondence, medicine, Humans, Prospective Studies, Copy-number variation, Prospective cohort study, Increased nuchal translucency, Allele frequency, Exome sequencing, 030304 developmental biology, 0303 health sciences, 030219 obstetrics & reproductive medicine, business.industry, Obstetrics, Patient Selection, Infant, Newborn, Obstetrics and Gynecology, General Medicine, Stillbirth, medicine.disease, 3. Good health, Abortion, Spontaneous, Developmental disorder, Phenotype, Female, Ultrasonography, Nuchal Translucency Measurement, business, Live Birth, Abortion, Eugenic, Cohort study
Abstract

Background Fetal structural anomalies, which are detected by ultrasonography, have a range of genetic causes, including chromosomal aneuploidy, copy number variations (CNVs; which are detectable by chromosomal microarrays), and pathogenic sequence variants in developmental genes. Testing for aneuploidy and CNVs is routine during the investigation of fetal structural anomalies, but there is little information on the clinical usefulness of genome-wide next-generation sequencing in the prenatal setting. We therefore aimed to evaluate the proportion of fetuses with structural abnormalities that had identifiable variants in genes associated with developmental disorders when assessed with whole-exome sequencing (WES). Methods In this prospective cohort study, two groups in Birmingham and London recruited patients from 34 fetal medicine units in England and Scotland. We used whole-exome sequencing (WES) to evaluate the presence of genetic variants in developmental disorder genes (diagnostic genetic variants) in a cohort of fetuses with structural anomalies and samples from their parents, after exclusion of aneuploidy and large CNVs. Women were eligible for inclusion if they were undergoing invasive testing for identified nuchal translucency or structural anomalies in their fetus, as detected by ultrasound after 11 weeks of gestation. The partners of these women also had to consent to participate. Sequencing results were interpreted with a targeted virtual gene panel for developmental disorders that comprised 1628 genes. Genetic results related to fetal structural anomaly phenotypes were then validated and reported postnatally. The primary endpoint, which was assessed in all fetuses, was the detection of diagnostic genetic variants considered to have caused the fetal developmental anomaly. Findings The cohort was recruited between Oct 22, 2014, and June 29, 2017, and clinical data were collected until March 31, 2018. After exclusion of fetuses with aneuploidy and CNVs, 610 fetuses with structural anomalies and 1202 matched parental samples (analysed as 596 fetus-parental trios, including two sets of twins, and 14 fetus-parent dyads) were analysed by WES. After bioinformatic filtering and prioritisation according to allele frequency and effect on protein and inheritance pattern, 321 genetic variants (representing 255 potential diagnoses) were selected as potentially pathogenic genetic variants (diagnostic genetic variants), and these variants were reviewed by a multidisciplinary clinical review panel. A diagnostic genetic variant was identified in 52 (8·5%; 95% CI 6·4–11·0) of 610 fetuses assessed and an additional 24 (3·9%) fetuses had a variant of uncertain significance that had potential clinical usefulness. Detection of diagnostic genetic variants enabled us to distinguish between syndromic and non-syndromic fetal anomalies (eg, congenital heart disease only vs a syndrome with congenital heart disease and learning disability). Diagnostic genetic variants were present in 22 (15·4%) of 143 fetuses with multisystem anomalies (ie, more than one fetal structural anomaly), nine (11·1%) of 81 fetuses with cardiac anomalies, and ten (15·4%) of 65 fetuses with skeletal anomalies; these phenotypes were most commonly associated with diagnostic variants. However, diagnostic genetic variants were least common in fetuses with isolated increased nuchal translucency (≥4·0 mm) in the first trimester (in three [3·2%] of 93 fetuses). Interpretation WES facilitates genetic diagnosis of fetal structural anomalies, which enables more accurate predictions of fetal prognosis and risk of recurrence in future pregnancies. However, the overall detection of diagnostic genetic variants in a prospectively ascertained cohort with a broad range of fetal structural anomalies is lower than that suggested by previous smaller-scale studies of fewer phenotypes. WES improved the identification of genetic disorders in fetuses with structural abnormalities; however, before clinical implementation, careful consideration should be given to case selection to maximise clinical usefulness. Funding UK Department of Health and Social Care and The Wellcome Trust.

Published
2019
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38. Genomics: the power, potential and pitfalls of the new technologies and how they are transforming healthcare

Author

Richard H Scott, Helen V Firth, Katherine S. Josephs, Katrina Tatton-Brown, Angela George, and Alison Berner

Subjects
Health professionals, business.industry, Emerging technologies, Genomic data, High-Throughput Nucleotide Sequencing, Genomics, General Medicine, 030204 cardiovascular system & hematology, Data science, Update, 03 medical and health sciences, 0302 clinical medicine, ComputingMethodologies_PATTERNRECOGNITION, Continuing medical education, Health care, Medicine, Humans, Education, Medical, Continuing, 030212 general & internal medicine, Precision Medicine, business, Delivery of Health Care
Abstract

Powerful new genomic technologies are transforming healthcare. The faster, cheaper generation of genomic data is driving the integration of genomics into all healthcare specialties. Within the next decade, healthcare professionals will be using genomic data to diagnose and manage their patients. However, despite these exciting advances, few clinicians are aware of or prepared for this genomics-based future. Through five patient-focused scenarios with accompanying interviews, this article showcases new genomic technologies while highlighting the inherent challenges associated with complex genomic data.

Published
2019

39. Phenotypic Spectrum of Seizure Disorders in MBD5-Associated Neurodevelopmental Disorder

Author

Julie Panetta, Ingrid E. Scheffer, Anna Rosati, Amy McTague, Richard H Scott, Renzo Guerrini, Carmen Barba, Heather C. Mefford, Chloe A Stutterd, Carvill Gl, John Nguyen, Kenneth A. Myers, Thorsten Stanley, Samantha Marin, and Carla Marini

Subjects
Pediatrics, medicine.medical_specialty, Microcephaly, Sleep disorder, Ataxia, business.industry, Status epilepticus, medicine.disease, Article, Epilepsy, Neurodevelopmental disorder, Intellectual disability, Epilepsy syndromes, medicine, Neurology (clinical), medicine.symptom, business, Genetics (clinical)
Abstract

ObjectiveTo describe the phenotypic spectrum in patients with MBD5-associated neurodevelopmental disorder (MAND) and seizures; features of MAND include intellectual disability, epilepsy, psychiatric features of aggression and hyperactivity, and dysmorphic features including short stature and microcephaly, sleep disturbance, and ataxia.MethodsWe performed phenotyping on patients with MBD5 deletions, duplications, or point mutations and a history of seizures.ResultsTwenty-three patients with MAND and seizures were included. Median seizure onset age was 2.9 years (range 3 days–13 years). The most common seizure type was generalized tonic-clonic; focal, atypical absence, tonic, drop attacks, and myoclonic seizures occurred frequently. Seven children had convulsive status epilepticus and 3 nonconvulsive status epilepticus. Fever, viral illnesses, and hot weather provoked seizures. EEG studies in 17/21 patients were abnormal, typically showing slow generalized spike-wave and background slowing. Nine had drug-resistant epilepsy, although 3 eventually became seizure-free. All but one had moderate-to-severe developmental impairment. Epilepsy syndromes included Lennox-Gastaut syndrome, myoclonic-atonic epilepsy, and infantile spasms syndrome. Behavioral problems in 20/23 included aggression, self-injurious behavior, and sleep disturbance.ConclusionsMBD5 disruption may be associated with severe early childhood-onset developmental and epileptic encephalopathy. Because neuropsychiatric dysfunction is common and severe, it should be an important focus of clinical management.

Published
2021
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40. Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease

Author

Keren J. Carss, Gavin Arno, Marie Erwood, Jonathan Stephens, Alba Sanchis-Juan, Sarah Hull, Karyn Megy, Detelina Grozeva, Eleanor Dewhurst, Samantha Malka, Vincent Plagnol, Christopher Penkett, Kathleen Stirrups, Roberta Rizzo, Genevieve Wright, Dragana Josifova, Maria Bitner-Glindzicz, Richard H. Scott, Emma Clement, Louise Allen, Ruth Armstrong, Angela F. Brady, Jenny Carmichael, Manali Chitre, Robert H.H. Henderson, Jane Hurst, Robert E. MacLaren, Elaine Murphy, Joan Paterson, Elisabeth Rosser, Dorothy A. Thompson, Emma Wakeling, Willem H. Ouwehand, Michel Michaelides, Anthony T. Moore, Andrew R. Webster, F. Lucy Raymond, Timothy Aitman, Hana Alachkar, Sonia Ali, David Allsup, Gautum Ambegaonkar, Julie Anderson, Richard Antrobus, Gururaj Arumugakani, Sofie Ashford, William Astle, Antony Attwood, Steve Austin, Chiara Bacchelli, Tamam Bakchoul, Tadbir K. Bariana, Helen Baxendale, David Bennett, Claire Bethune, Shahnaz Bibi, Marta Bleda, Harm Boggard, Paula Bolton-Maggs, Claire Booth, John R. Bradley, Angie Brady, Matthew Brown, Michael Browning, Christine Bryson, Siobhan Burns, Paul Calleja, Natalie Canham, Keren Carss, Mark Caulfield, Elizabeth Chalmers, Anita Chandra, Patrick Chinnery, Colin Church, Naomi Clements-Brod, Virginia Clowes, Gerry Coghlan, Peter Collins, Nichola Cooper, Amanda Creaser-Myers, Rosa DaCosta, Louise Daugherty, Sophie Davies, John Davis, Minka De Vries, Patrick Deegan, Sri V.V. Deevi, Charu Deshpande, Lisa Devlin, Rainer Doffinger, Natalie Dormand, Elizabeth Drewe, David Edgar, William Egner, Wendy N. Erber, Tamara Everington, Remi Favier, Helen Firth, Debra Fletcher, Frances Flinter, James C. Fox, Amy Frary, Kathleen Freson, Bruce Furie, Abigail Furnell, Daniel Gale, Alice Gardham, Michael Gattens, Neeti Ghali, Pavandeep K. Ghataorhe, Rohit Ghurye, Simon Gibbs, Kimberley Gilmour, Paul Gissen, Sarah Goddard, Keith Gomez, Pavel Gordins, Stefan Gräf, Daniel Greene, Alan Greenhalgh, Andreas Greinacher, Sofia Grigoriadou, Scott Hackett, Charaka Hadinnapola, Rosie Hague, Matthias Haimel, Csaba Halmagyi, Tracey Hammerton, Daniel Hart, Grant Hayman, Johan W.M. Heemskerk, Robert Henderson, Anke Hensiek, Yvonne Henskens, Archana Herwadkar, Simon Holden, Muriel Holder, Susan Holder, Fengyuan Hu, Aarnoud Huissoon, Marc Humbert, Roger James, Stephen Jolles, Rashid Kazmi, David Keeling, Peter Kelleher, Anne M. Kelly, Fiona Kennedy, David Kiely, Nathalie Kingston, Ania Koziell, Deepa Krishnakumar, Taco W. Kuijpers, Dinakantha Kumararatne, Manju Kurian, Michael A. Laffan, Michele P. Lambert, Hana Lango Allen, Allan Lawrie, Sara Lear, Melissa Lees, Claire Lentaigne, Ri Liesner, Rachel Linger, Hilary Longhurst, Lorena Lorenzo, Rajiv Machado, Rob Mackenzie, Robert MacLaren, Eamonn Maher, Jesmeen Maimaris, Sarah Mangles, Ania Manson, Rutendo Mapeta, Hugh S. Markus, Jennifer Martin, Larahmie Masati, Mary Mathias, Vera Matser, Anna Maw, Elizabeth McDermott, Coleen McJannet, Stuart Meacham, Sharon Meehan, Sarju Mehta, Carolyn M. Millar, Shahin Moledina, Anthony Moore, Nicholas Morrell, Andrew Mumford, Sai Murng, Sergey Nejentsev, Sadia Noorani, Paquita Nurden, Eric Oksenhendler, Sofia Papadia, Soo-Mi Park, Alasdair Parker, John Pasi, Chris Patch, Jeanette Payne, Andrew Peacock, Kathelijne Peerlinck, Christopher J. Penkett, Joanna Pepke-Zaba, David J. Perry, Val Pollock, Gary Polwarth, Mark Ponsford, Waseem Qasim, Isabella Quinti, Stuart Rankin, Julia Rankin, Karola Rehnstrom, Evan Reid, Christopher J. Rhodes, Michael Richards, Sylvia Richardson, Alex Richter, Irene Roberts, Matthew Rondina, Catherine Roughley, Kevin Rue-Albrecht, Crina Samarghitean, Richard Sandford, Saikat Santra, Ravishankar Sargur, Sinisa Savic, Sol Schulman, Harald Schulze, Richard Scott, Marie Scully, Suranjith Seneviratne, Carrock Sewell, Olga Shamardina, Debbie Shipley, Ilenia Simeoni, Suthesh Sivapalaratnam, Kenneth Smith, Aman Sohal, Laura Southgate, Simon Staines, Emily Staples, Hans Stauss, Penelope Stein, Sophie Stock, Jay Suntharalingam, R. Campbell Tait, Kate Talks, Yvonne Tan, Jecko Thachil, James Thaventhiran, Ellen Thomas, Moira Thomas, Dorothy Thompson, Adrian Thrasher, Marc Tischkowitz, Catherine Titterton, Cheng-Hock Toh, Mark Toshner, Carmen Treacy, Richard Trembath, Salih Tuna, Wojciech Turek, Ernest Turro, Chris Van Geet, Marijke Veltman, Julie Vogt, Julie von Ziegenweldt, Anton Vonk Noordegraaf, Ivy Wanjiku, Timothy Q. Warner, Evangeline Wassmer, Hugh Watkins, Andrew Webster, Steve Welch, Sarah Westbury, John Wharton, Deborah Whitehorn, Martin Wilkins, Lisa Willcocks, Catherine Williamson, Geoffrey Woods, John Wort, Nigel Yeatman, Patrick Yong, Tim Young, Ping Yu, Pediatric surgery, Molecular cell biology and Immunology, Pulmonary medicine, ACS - Pulmonary hypertension & thrombosis, APH - Quality of Care, Amsterdam Reproduction & Development (AR&D), Rue-Albrecht, K, RS: CARIM - R1.04 - Clinical thrombosis and haemostasis, MUMC+: DA CDL Algemeen (9), Med Microbiol, Infect Dis & Infect Prev, RS: CARIM - R1.03 - Cell biochemistry of thrombosis and haemostasis, Biochemie, Raymond, Lucy [0000-0003-2652-3355], Apollo - University of Cambridge Repository, Vascular Medicine, and Paediatric Infectious Diseases / Rheumatology / Immunology

Subjects
0301 basic medicine, Male, DNA Mutational Analysis, EXOME, PROTEIN, Eye, whole-genome sequence, NIHR-BioResource Rare Diseases Consortium, Medical and Health Sciences, Choroideremia, ACTIVATION, 0302 clinical medicine, Ethnicity, 2.1 Biological and endogenous factors, Exome, rare sequence variant, Copy-number variation, Aetiology, MUTATION, Genetics (clinical), Exome sequencing, Genetics & Heredity, Genetics, Genome, Adaptor Proteins, Biological Sciences, DYSTROPHY, copy-number variants, Female, Human, Common disease-common variant, LEBER CONGENITAL AMAUROSIS, Ethnic Groups, Genes, Recessive, Biology, DIAGNOSIS, Article, 03 medical and health sciences, Rare Diseases, Retinal Diseases, STARGARDT DISEASE, Clinical Research, REVEALS, Journal Article, medicine, Recessive, Humans, retinal dystrophy, Eye Disease and Disorders of Vision, Alleles, Adaptor Proteins, Signal Transducing, Whole genome sequencing, Base Sequence, Genome, Human, Human Genome, Signal Transducing, Neurosciences, Genetic Variation, medicine.disease, GENE, Introns, Stargardt disease, Good Health and Well Being, 030104 developmental biology, Genes, Mutation, 030221 ophthalmology & optometry, Human genome
Abstract

Inherited retinal disease is a common cause of visual impairment and represents a highly heterogeneous group of conditions. Here, we present findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing (n = 605), whole-exome sequencing (n = 72), or both (n = 45) performed, as part of the NIHR-BioResource Rare Diseases research study. We identified pathogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) individuals. Whole-genome sequencing gives unprecedented power to detect three categories of pathogenic variants in particular: structural variants, variants in GC-rich regions, which have significantly improved coverage compared to whole-exome sequencing, and variants in non-coding regulatory regions. In addition to previously reported pathogenic regulatory variants, we have identified a previously unreported pathogenic intronic variant in $\textit{CHM}$ in two males with choroideremia. We have also identified 19 genes not previously known to be associated with inherited retinal disease, which harbor biallelic predicted protein-truncating variants in unsolved cases. Whole-genome sequencing is an increasingly important comprehensive method with which to investigate the genetic causes of inherited retinal disease.

Published
2017
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41. The Human Phenotype Ontology in 2017

Author

Rachel Thompson, Stanley J. F. Laulederkind, Richard H. Scott, Panagiotis I. Sergouniotis, Ada Hamosh, Mark Engelstad, Hanns Lochmüller, Gareth Baynam, Richard Sever, Roger James, Hugh Dawkins, Laureen E. Connell, C. Turner, Andrew D. Devereau, Susan M. Bello, Michael Brudno, Courtney Hum, Cynthia L. Smith, Julie A. McMurry, Michael M. Segal, Damian Smedley, Gholson J. Lyon, Helen V. Firth, Ingo Helbig, Tom Vulliamy, Roland Krause, Patrick F. Chinnery, Franz Schaefer, Ernest Turro, Melissa A. Haendel, Cornelius F. Boerkoel, Peter N. Robinson, Willem H. Ouwehand, Orion J. Buske, Kym M. Boycott, Volker Straub, Bert B.A. de Vries, Daniel Greene, Valentina Cipriani, Erin D. Foster, Annie Olry, Julius O.B. Jacobsen, Laura E. DeMare, Marijcke W. M. Veltman, Nikolas Pontikos, Andreas Zankl, Tudor Groza, Kathleen Freson, Sebastian Köhler, Ana Rath, Nicole Vasilevsky, Julie von Ziegenweidt, Ségolène Aymé, Soichi Ogishima, Johanna A. Jähn, Jing Yu, Tomasz Zemojtel, Stephan Züchner, and Christopher J. Mungall

Subjects
0301 basic medicine, Multidisciplinaire, généralités & autres [D99] [Sciences de la santé humaine], Genomics, Translational research, Computational biology, Biology, Ontology (information science), Terminology, Translational Research, Biomedical, 03 medical and health sciences, Rare Diseases, Human Phenotype Ontology, Genetics, Database Issue, Humans, Precision Medicine, Multidisciplinary, general & others [D99] [Human health sciences], Genetic Association Studies, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Computational Biology, Biological Ontologies, Precision medicine, Phenotype, 3. Good health, 030104 developmental biology, Algorithms, Software
Abstract

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology. ispartof: Nucleic Acids Research vol:45 issue:D1 pages:D865-D876 ispartof: location:England status: published

Published
2016
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42. Clinical and Functional Characterization of the Recurrent TUBA1A p.(Arg2His) Mutation

Author

Férechté Encha-Razavi, Sakkubai Naidu, Tania Attié-Bitach, Daniela T. Pilz, Neil Stoodley, Andrew E. Fry, Heather E. Olson, Jennifer Gardner, Sheila Palmer-Smith, Georgios Niotakis, Thomas D. Cushion, Julie S. Cohen, Hood Mugalaasi, Jonathan G. L. Mullins, Lucile Boutaud, Richard H Scott, Maryse Bonnières, and P. Grant

Subjects
0301 basic medicine, Microcephaly, cerebellar hypoplasia, TUBA1A, Context (language use), Biology, Corpus callosum, Article, lcsh:RC321-571, 03 medical and health sciences, 0302 clinical medicine, Polymicrogyria, medicine, Missense mutation, polymicrogyria, lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry, Genetics, General Neuroscience, medicine.disease, Perisylvian polymicrogyria, tubulinopathy, p.(Arg2His), R2H, 030104 developmental biology, tubulin, Mutation (genetic algorithm), Cerebellar vermis, 030217 neurology & neurosurgery
Abstract

The TUBA1A gene encodes tubulin alpha-1A, a protein that is highly expressed in the fetal brain. Alpha- and beta-tubulin subunits form dimers, which then co-assemble into microtubule polymers: dynamic, scaffold-like structures that perform key functions during neurogenesis, neuronal migration, and cortical organisation. Mutations in TUBA1A have been reported to cause a range of brain malformations. We describe four unrelated patients with the same de novo missense mutation in TUBA1A, c.5G&gt, A, p.(Arg2His), as found by next generation sequencing. Detailed comparison revealed similar brain phenotypes with mild variability. Shared features included developmental delay, microcephaly, hypoplasia of the cerebellar vermis, dysplasia or thinning of the corpus callosum, small pons, and dysmorphic basal ganglia. Two of the patients had bilateral perisylvian polymicrogyria. We examined the effects of the p.(Arg2His) mutation by computer-based protein structure modelling and heterologous expression in HEK-293 cells. The results suggest the mutation subtly impairs microtubule function, potentially by affecting inter-dimer interaction. Based on its sequence context, c.5G&gt, A is likely to be a common recurrent mutation. We propose that the subtle functional effects of p.(Arg2His) may allow for other factors (such as genetic background or environmental conditions) to influence phenotypic outcome, thus explaining the mild variability in clinical manifestations.

Published
2018

43. Exome sequencing for prenatal diagnosis of fetuses with sonographic abnormalities

Author

Richard H Scott, Suzanne Drury, Lyn S. Chitty, Natalie Trump, Nicholas Lench, Christopher Boustred, and Hywel Williams

Subjects
Pathology, medicine.medical_specialty, business.industry, Hypophosphatasia, Obstetrics and Gynecology, Aneuploidy, Prenatal diagnosis, medicine.disease, medicine.anatomical_structure, Nuchal Translucency Measurement, embryonic structures, medicine, Chorionic villi, business, Exome, Increased nuchal translucency, Genetics (clinical), Exome sequencing
Abstract

Objective In the absence of aneuploidy or other pathogenic cytogenetic abnormality, fetuses with increased nuchal translucency (NT ≥ 3.5 mm) and/or other sonographic abnormalities have a greater incidence of genetic syndromes, but defining the underlying pathology can be challenging. Here, we investigate the value of whole exome sequencing in fetuses with sonographic abnormalities but normal microarray analysis. Method Whole exome sequencing was performed on DNA extracted from chorionic villi or amniocytes in 24 fetuses with unexplained ultrasound findings. In the first 14 cases sequencing was initially performed on fetal DNA only. For the remaining 10, the trio of fetus, mother and father was sequenced simultaneously. Results In 21% (5/24) cases, exome sequencing provided definitive diagnoses (Milroy disease, hypophosphatasia, achondrogenesis type 2, Freeman–Sheldon syndrome and Baraitser–Winter Syndrome). In a further case, a plausible diagnosis of orofaciodigital syndrome type 6 was made. In two others, a single mutation in an autosomal recessive gene was identified, but incomplete sequencing coverage precluded exclusion of the presence of a second mutation. Conclusion Whole exome sequencing improves prenatal diagnosis in euploid fetuses with abnormal ultrasound scans. In order to expedite interpretation of results, trio sequencing should be employed, but interpretation can still be compromised by incomplete coverage of relevant genes. © 2015 John Wiley & Sons, Ltd.

Published
2015
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44. Mecom-Associated Syndrome: A Heterogeneous Inherited Bone Marrow Failure Syndrome With Amegakaryocytic Thrombocytopenia

Author

Sule Unal, Phil Ancliff, Dirk Schwabe, Richard H Scott, Jaime Estrada, Matthias Ballmaier, Markus Metzler, Horst Rütschle, Eva Ponstingl, Manuela Germeshausen, Bernward Zeller, Angela Wawer, and Çocuk Sağlığı ve Hastalıkları

Subjects
0301 basic medicine, Male, Pathology, medicine.medical_specialty, Clinodactyly, MECOM, Hearing loss, Anemia, Hematopoiesis and Stem Cells, Hemoglobinuria, Paroxysmal, 03 medical and health sciences, Genetic Heterogeneity, medicine, Congenital Bone Marrow Failure Syndromes, Humans, Genetic Predisposition to Disease, Bone Marrow Diseases, Genetic Association Studies, business.industry, Genetic heterogeneity, Bone marrow failure, Anemia, Aplastic, Hematology, Bone Marrow Failure Disorders, medicine.disease, Hematopoietic Stem Cells, Pancytopenia, Thrombocytopenia, Lymphocyte Subsets, MDS1 and EVI1 Complex Locus Protein, Pedigree, DNA-Binding Proteins, 030104 developmental biology, Mutation, Congenital amegakaryocytic thrombocytopenia, Female, medicine.symptom, business, Transcription Factors
Abstract

Heterozygous mutations in MECOM (MDS1 and EVI1 complex locus) have been reported to be causative of a rare association of congenital amegakaryocytic thrombocytopenia and radioulnar synostosis. Here we report on 12 patients with congenital hypomegakaryocytic thrombocytopenia caused by MECOM mutations (including 10 novel mutations). The mutations affected different functional domains of the EVI1 protein. The spectrum of phenotypes was much broader than initially reported for the first 3 patients; we found familial as well as sporadic cases, and the clinical spectrum ranged from isolated radioulnar synostosis with no or mild hematological involvement to severe bone marrow failure without obvious skeletal abnormality. The clinical picture included radioulnar synostosis, bone marrow failure, clinodactyly, cardiac and renal malformations, B-cell deficiency, and presenile hearing loss. No single clinical manifestation was detected in all patients affected by MECOM mutations. Radioulnar synostosis and B-cell deficiency were observed only in patients with mutations affecting a short region in the C-terminal zinc finger domain of EVI1. We propose the term MECOM-associated syndrome for this heterogeneous hereditary disease and inclusion of MECOM sequencing in the diagnostic workup of congenital bone marrow failure.

Published
2018

45. A Recurrent De Novo Nonsense Variant in ZSWIM6 Results in Severe Intellectual Disability without Frontonasal or Limb Malformations

Author

Susan Brammah, Honey Nagakura, Christopher T. Gordon, Laurence Hubert, Andrea M. Lewis, Renee Carroll, Richard H. Scott, Alexandrine Garrigue, Melanie Leffler, Jozef Gecz, Michael Field, Lucinda Murray, Sarah Risen, Seema R. Lalani, Marie Shaw, Geneviève de Saint Basile, Augusto Rendon, Raman Kumar, Tracy Dudding-Byth, LaDonna Immken, Patrick Nitschké, Arnold Munnich, Jeanne Amiel, Mark J. Cowley, Judy Spies, Bronwyn Kerr, Myriam Oufadem, Nina Powell-Hamilton, Claude Besmond, John D. Pollard, Emma Kivuva, Christine Bole-Feysot, William G. Newman, Jill A. Rosenfeld, Elizabeth E. Palmer, Jessica Tusi, Allison Tam, Richard Webster, Francesca Filippini, Marlène Rio, André E. Minoche, and Fan Xia

Subjects
0301 basic medicine, Central Nervous System, media_common.quotation_subject, Nonsense, Limb Deformities, Congenital, Neurocognitive Disorders, Bioinformatics, 03 medical and health sciences, Exon, Report, Intellectual Disability, Intellectual disability, Peripheral Nervous System, Genetics, medicine, Journal Article, Missense mutation, Humans, Craniofacial, Gene, Genetics (clinical), media_common, business.industry, High-Throughput Nucleotide Sequencing, medicine.disease, Phenotype, DNA-Binding Proteins, 030104 developmental biology, medicine.anatomical_structure, Codon, Nonsense, Peripheral nervous system, business, Mandibulofacial Dysostosis
Abstract

A recurrent de novo missense variant within the C-terminal Sin3-like domain of ZSWIM6 was previously reported to cause acromelic frontonasal dysostosis (AFND), an autosomal-dominant severe frontonasal and limb malformation syndrome, associated with neurocognitive and motor delay, via a proposed gain-of-function effect. We present detailed phenotypic information on seven unrelated individuals with a recurrent de novo nonsense variant (c.2737C>T [p.Arg913Ter]) in the penultimate exon of ZSWIM6 who have severe-profound intellectual disability and additional central and peripheral nervous system symptoms but an absence of frontonasal or limb malformations. We show that the c.2737C>T variant does not trigger nonsense-mediated decay of the ZSWIM6 mRNA in affected individual-derived cells. This finding supports the existence of a truncated ZSWIM6 protein lacking the Sin3-like domain, which could have a dominant-negative effect. This study builds support for a key role for ZSWIM6 in neuronal development and function, in addition to its putative roles in limb and craniofacial development, and provides a striking example of different variants in the same gene leading to distinct phenotypes.

Published
2017
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46. The rise of the genome and personalised medicine

Author

Ellen Thomas, Helen K. Brittain, and Richard H Scott

Subjects
0301 basic medicine, Service (systems architecture), Psychological intervention, Genomics, Genetic Counseling, Disease, 030105 genetics & heredity, Mainstreaming, Genome, State Medicine, 03 medical and health sciences, Neoplasms, Medicine, Humans, Ethics, Medical, Genetic Predisposition to Disease, Genetic Testing, Precision Medicine, Genetic testing, Whole genome sequencing, Medical education, medicine.diagnostic_test, Whole Genome Sequencing, business.industry, Genome, Human, General Medicine, United Kingdom, CME Genetic medicine, business
Abstract

Virtually all medical specialties are impacted by genetic disease. Enhanced understanding of the role of genetics in human disease, coupled with rapid advancement in sequencing technology, is transforming the speed of diagnosis for patients and providing increasing opportunities to tailor management. As set out in the Annual report of the Chief Medical Officer 2016: Generation Genome1 and the recent NHS England board paper Creating a genomic medicine service to lay the foundations to deliver personalised interventions and treatments,2 the increasing 'mainstreaming' of genetic testing into routine practice and plans to embed whole genome sequencing in the NHS mean that the profile and importance of genomics is on the rise for many clinicians. This article provides a brief overview of genomics and its current clinical applications, including its contribution to personalised medicine. Physicians will be signposted to key issues that will allow the successful implementation of genomics for rare disease diagnosis and cancer management.

Published
2017

47. Germline mutations affecting the histone H4 core cause a developmental syndrome by altering DNA damage response and cell cycle control

Author

Federico Tessadori, Harmjan R. Vos, Jeroen Bakkers, Richard H Scott, Karen Duran, Jane A. Hurst, Koen L.I. van Gassen, Maarten P.G. Massink, Robert M. van Es, Gijs van Haaften, Jacques C. Giltay, and Hubrecht Institute for Developmental Biology and Stem Cell Research

Subjects
0301 basic medicine, Embryo, Nonmammalian, DNA Repair, Developmental Disabilities, Apoptosis, Diseases, Histones, 0302 clinical medicine, Histone methylation, Histone code, Developmental, Cancer epigenetics, Child, Zebrafish, Epigenomics, Genetics, Nonmammalian, biology, Neurodevelopmental disorders, Gene Expression Regulation, Developmental, Syndrome, Nucleosomes, Histone, Embryo, 030220 oncology & carcinogenesis, Histone methyltransferase, Embryogenesis, Microcephaly, Female, Adolescent, Mutation, Missense, Genomic Instability, Histone H4, 03 medical and health sciences, Intellectual Disability, Histone H2A, Developmental biology, Journal Article, Animals, Humans, Germ-Line Mutation, Infant, Cell Cycle Checkpoints, 030104 developmental biology, Gene Expression Regulation, Mutation, biology.protein, Missense, DNA Damage
Abstract

Covalent modifications of histones have an established role as chromatin effectors, as they control processes such as DNA replication and transcription, and repair or regulate nucleosomal structure. Loss of modifications on histone N tails, whether due to mutations in genes belonging to histone-modifying complexes or mutations directly affecting the histone tails, causes developmental disorders or has a role in tumorigenesis. More recently, modifications affecting the globular histone core have been uncovered as being crucial for DNA repair, pluripotency and oncogenesis. Here we report monoallelic missense mutations affecting lysine 91 in the histone H4 core (H4K91) in three individuals with a syndrome of growth delay, microcephaly and intellectual disability. Expression of the histone H4 mutants in zebrafish embryos recapitulates the developmental anomalies seen in the patients. We show that the histone H4 alterations cause genomic instability, resulting in increased apoptosis and cell cycle progression anomalies during early development. Mechanistically, our findings indicate an important role for the ubiquitination of H4K91 in genomic stability during embryonic development.

Published
2017

48. B2.4 Rapid paediatric sequencing (raps) in critically ill children at great ormond street hospital

Author

P Beales, Jane A. Hurst, H Williams, L Boukhibar, Wendy D Jones, Richard H Scott, Emma Clement, Lyn S. Chitty, Maria Bitner-Glindzicz, and Mark J. Peters

Subjects
medicine.medical_specialty, Pediatrics, business.industry, Critically ill, Complex disease, Turnaround time, Unmet needs, Intensive care, Medicine, Personalized medicine, Sample collection, business, Intensive care medicine, Point of care
Abstract

Background Great Ormond Street Hospital cares for many children with rare and complex disease. A substantial proportion of these children will have an underlying genetic cause for their condition. Making a diagnosis in such cases is increasingly achievable due to advances in genomic testing. However, such testing may not be available on the NHS and results, when accessed in the research setting, typically take many months to report. In critically ill children, cared for on the intensive care units, a timely genetic diagnosis may be beneficial on a number of levels. It may inform treatment options and prognosis. It may also reduce the need for further investigations, improving the diagnostic odyssey and potentially reducing costs. In addition, it may help the family understand recurrence risks. Methods To address this unmet need we developed a work flow to enable Rapid Paediatric Sequencing (RaPS) in critically ill children. Eligible patient-parent trios were recruited and underwent whole genome sequencing. A framework was developed to allow capture of clinical information and robust analysis of genomic data initially by investigating candidate gene lists and HPO-derived panels. If no genetic diagnosis was forthcoming, genomic analysis was broadened and more disease-causing genes were investigated. Results Twenty two patient-parent trios were recruited to the RaPS pilot project. A diagnosis was reached in 8 cases (36%). The shortest turnaround time from sample collection to return of provisional results was 5 days. A genetic diagnosis informed point of care decisions in at least 3 cases. Conclusion We report on the process and framework necessary to deliver rapid whole genome sequencing to critically ill paediatric patients and reflect on the outcomes, clinical utility and challenges of implementing such a service at GOSH.

Published
2017
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49. B2.1 100,000 genomes project at gosh: experience from 111 pilot families

Author

S Loughlin, Emma Clement, P Beales, Lucy Jenkins, Emma Ashton, Richard H Scott, Maria Bitner-Glindzicz, and Andrew Buckton

Subjects
Proband, medicine.medical_specialty, Likely benign, business.industry, Family medicine, Medicine, Genomics, In patient, Genetic diagnosis, business, Genome, Likely pathogenic, Rare disease
Abstract

Background The 100,000 Genomes Project is a national programme to perform whole genome sequencing (WGS) in families with an undiagnosed rare disorder or cancer. Multiple specialties from GOSH have recruited patients to the pilot study. Here we report on the outcome of the first 111 pilot cases. Methodology Total lymphocyte DNA was extracted (Chemagic Star, Chemagen) and exported to Genomics England for WGS (HiSeqX, Illumina). Prioritised variants were discussed and classified by a multidisciplinary team (MDT) of Clinical Scientists, Consultant Clinical Geneticists and the recruiting clinicians. Variants deemed to be ‘pathogenic’ or ‘likely pathogenic’ were flagged for diagnostic confirmation and clinical reporting. Results Genomics England returned results for 111 cases (probands); 95 (86%) were analysed as trios (proband and both parents). Variant interpretation has been completed for 97 cases (87%). Thirty-six percent of cases (40/111) and a total of 76 variants were discussed at an MDT meeting. Fifty-three percent of variants discussed (40/76) were classified as pathogenic or likely pathogenic, 30% (23/76) were classified as variants of unknown significance and 17% (13/76) were classified as benign or likely benign. This equated to a genetic diagnosis in 27/111 cases (25%) of which 5/111 (5%) were felt to be a partial rather than full explanation of the phenotype. Of the 97 cases where primary analysis was complete, 66/97 (68%) had no primary findings. This included cases in which variants of unknown significance have been detected. Conclusion WGS is a useful tool for rare disease diagnosis especially in patients who have undergone a fruitless diagnostic odyssey. Analysis of GOSH pilot cases has enabled us to develop infrastructure locally to support the return of main programme results. One quarter of GOSH pilot patients should expect a genetic diagnosis from the primary analysis. It is unclear whether this will be an accurate reflection of the diagnostic rate achieved in the main programme due to ongoing refinement of the recruitment and analysis pipelines.

Published
2017
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50. Contiguous gene deletion of TBX5 and TBX3: report of another case

Author

Robert W. Yates, Morgan R. Keane, Richard H Scott, Drew Ellershaw, Patricia A. Foley, Gill D. Smith, Alistair Calder, Caroline E. Brain, and Francesca Forzano

Subjects
0301 basic medicine, Genetics, Heart Defects, Congenital, business.industry, General Medicine, 030105 genetics & heredity, Gene deletion, Heart Septal Defects, Atrial, Pathology and Forensic Medicine, 03 medical and health sciences, 030104 developmental biology, Pediatrics, Perinatology and Child Health, Medicine, Humans, Abnormalities, Multiple, Female, Upper Extremity Deformities, Congenital, Anatomy, business, Child, T-Box Domain Proteins, Genetics (clinical), Gene Deletion, Lower Extremity Deformities, Congenital
Published
2017

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